Admin menu links missing after module activation

I've encountered a series of strange Problems ending up in most links missing in my admin menu trying to accomplish what I've described here: http://drupal.org/node/363887.

The following steps led to the current situation:

- Module trigger deactivated
- Module rules (http://drupal.org/project/rules) installed
- The /admin page was no longer reachable (Error 500)
- I deactivated the module "rules" according to this description: http://drupal.org/node/45563
- The /admin page was reachable again.
- Thinking that the problems with installing "rules" could actually be about the recent deactivation of "trigger" I reenabled "trigger" via the regular modules menu.
- Error 500 for all /admin pages again
- cron ran
- /admin was reachable showing the following error:

    * user warning: Duplicate entry 'themes/pushbutton/pushbutton.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('pushbutton', 'themes/engines/phptemplate/phptemplate.engine', 'a:13:{s:4:\"name\";s:10:\"Pushbutton\";s:11:\"description\";s:52:\"Tabled, multi-column theme in blue and orange tones.\";s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:6:\"engine\";s:11:\"phptemplate\";s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:7:\"regions\";a:5:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";s:7:\"content\";s:7:\"Content\";s:6:\"header\";s:6:\"Header\";s:6:\"footer\";s:6:\"Footer\";}s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:11:\"stylesheets\";a:1:{s:3:\"all\";a:1:{s:9:\"style.css\";s:27:\"themes/pushbutton/style.css\";}}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:27:\"themes/pushbutton/script.js\";}s:10:\"screenshot\";s:32:\"themes/pushbutton/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";}', 'theme', 'themes/pushbutton/pushbutton.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.
    * user warning: Duplicate entry 'themes/garland/minnelli/minnelli.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('minnelli', 'themes/engines/phptemplate/phptemplate.engine', 'a:14:{s:4:\"name\";s:8:\"Minnelli\";s:11:\"description\";s:56:\"Tableless, recolorable, multi-column, fixed width theme.\";s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:10:\"base theme\";s:7:\"garland\";s:11:\"stylesheets\";a:1:{s:3:\"all\";a:1:{s:12:\"minnelli.css\";s:36:\"themes/garland/minnelli/minnelli.css\";}}s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:7:\"regions\";a:5:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";s:7:\"content\";s:7:\"Content\";s:6:\"header\";s:6:\"Header\";s:6:\"footer\";s:6:\"Footer\";}s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:33:\"themes/garland/minnelli/script.js\";}s:10:\"screenshot\";s:38:\"themes/garland/minnelli/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";s:6:\"engine\";s:11:\"phptemplate\";}', 'theme', 'themes/garland/minnelli/minnelli.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.
    * user warning: Duplicate entry 'themes/garland/garland.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('garland', 'themes/engines/phptemplate/phptemplate.engine', 'a:13:{s:4:\"name\";s:7:\"Garland\";s:11:\"description\";s:66:\"Tableless, recolorable, multi-column, fluid width theme (default).\";s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:6:\"engine\";s:11:\"phptemplate\";s:11:\"stylesheets\";a:2:{s:3:\"all\";a:1:{s:9:\"style.css\";s:24:\"themes/garland/style.css\";}s:5:\"print\";a:1:{s:9:\"print.css\";s:24:\"themes/garland/print.css\";}}s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:7:\"regions\";a:5:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";s:7:\"content\";s:7:\"Content\";s:6:\"header\";s:6:\"Header\";s:6:\"footer\";s:6:\"Footer\";}s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:24:\"themes/garland/script.js\";}s:10:\"screenshot\";s:29:\"themes/garland/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";}', 'theme', 'themes/garland/garland.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.
    * user warning: Duplicate entry 'themes/chameleon/marvin/marvin.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('marvin', '', 'a:13:{s:4:\"name\";s:6:\"Marvin\";s:11:\"description\";s:31:\"Boxy tabled theme in all grays.\";s:7:\"regions\";a:2:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";}s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:10:\"base theme\";s:9:\"chameleon\";s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:11:\"stylesheets\";a:1:{s:3:\"all\";a:1:{s:9:\"style.css\";s:33:\"themes/chameleon/marvin/style.css\";}}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:33:\"themes/chameleon/marvin/script.js\";}s:10:\"screenshot\";s:38:\"themes/chameleon/marvin/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";}', 'theme', 'themes/chameleon/marvin/marvin.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.
    * user warning: Duplicate entry 'themes/chameleon/chameleon.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('chameleon', 'themes/chameleon/chameleon.theme', 'a:12:{s:4:\"name\";s:9:\"Chameleon\";s:11:\"description\";s:42:\"Minimalist tabled theme with light colors.\";s:7:\"regions\";a:2:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";}s:8:\"features\";a:4:{i:0;s:4:\"logo\";i:1;s:7:\"favicon\";i:2;s:4:\"name\";i:3;s:6:\"slogan\";}s:11:\"stylesheets\";a:1:{s:3:\"all\";a:2:{s:9:\"style.css\";s:26:\"themes/chameleon/style.css\";s:10:\"common.css\";s:27:\"themes/chameleon/common.css\";}}s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:7:\"scripts\";a:1:{s:9:\"script.js\";s:26:\"themes/chameleon/script.js\";}s:10:\"screenshot\";s:31:\"themes/chameleon/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";}', 'theme', 'themes/chameleon/chameleon.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.
    * user warning: Duplicate entry 'themes/bluemarine/bluemarine.info' for key 1 query: INSERT INTO system (name, owner, info, type, filename, status, throttle, bootstrap) VALUES ('bluemarine', 'themes/engines/phptemplate/phptemplate.engine', 'a:13:{s:4:\"name\";s:10:\"Bluemarine\";s:11:\"description\";s:66:\"Table-based multi-column theme with a marine and ash color scheme.\";s:7:\"version\";s:3:\"6.9\";s:4:\"core\";s:3:\"6.x\";s:6:\"engine\";s:11:\"phptemplate\";s:7:\"project\";s:6:\"drupal\";s:9:\"datestamp\";s:10:\"1231976413\";s:7:\"regions\";a:5:{s:4:\"left\";s:12:\"Left sidebar\";s:5:\"right\";s:13:\"Right sidebar\";s:7:\"content\";s:7:\"Content\";s:6:\"header\";s:6:\"Header\";s:6:\"footer\";s:6:\"Footer\";}s:8:\"features\";a:10:{i:0;s:20:\"comment_user_picture\";i:1;s:7:\"favicon\";i:2;s:7:\"mission\";i:3;s:4:\"logo\";i:4;s:4:\"name\";i:5;s:17:\"node_user_picture\";i:6;s:6:\"search\";i:7;s:6:\"slogan\";i:8;s:13:\"primary_links\";i:9;s:15:\"secondary_links\";}s:11:\"stylesheets\";a:1:{s:3:\"all\";a:1:{s:9:\"style.css\";s:27:\"themes/bluemarine/style.css\";}}s:7:\"scripts\";a:1:{s:9:\"script.js\";s:27:\"themes/bluemarine/script.js\";}s:10:\"screenshot\";s:32:\"themes/bluemarine/screenshot.png\";s:3:\"php\";s:5:\"4.3.5\";}', 'theme', 'themes/bluemarine/bluemarine.info', 0, 0, 0) in /mnt/web2/52/05/5745645/htdocs/35234523/modules/system/system.module on line 821.

- now most links in /admin (for example "modules") are missing

Can anyone help?

Thank You