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7.9 to 7.17 core update, system links not using base url

I've recently updated core from 7.9 to 7.17. Things seem to be working correctly, except, all system generated links are no longer recognizing the correct base path. I have my install in a subdirectory so the base path is mydomain/subdirectory. No problems in 7.9, but now all system generated (including menu) links only render the top level/root (thus excluding 'subdirectory') as the base url. The htaccess file is working correctly (as is clean url's). And drupal is rendering the correct base_url when I test print the $base_url. Any ideas?

Comments

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when you updated did you overwrite the the 7.9 .htaccess? if so; drop the 7.9 .htaccess into the 7.16 install and test. If it works then compare the two files.

No, didn't overwrite it. Did

No, didn't overwrite it. Did diff the two and they are virtually identical. Tried small changes but no difference. It doesn't seem like an htaccess issue. Manual links work fine. Only drupal generated links don't. Haven't experienced anything quite like this before.
Also cleared caches many times.

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the only other thing I can think would be settings.php where $base_url is set, does it include the subdirectory?

Yes, it does. The menu

Yes, it does. The menu system appears to be the culprate. All asset files (css, javascript, etc) are called correctly.

It appears to actually be an

It appears to actually be an issue with the core Locale module. It's a multilingual site so upon uninstalling Locale, link items work correctly.

It appears to be a url bug in

It appears to be a url bug in the locale.inc file, starting at version 7.14. This solved the issue. #1826252: Domain language negotiation broken when a base url is configured

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