Sometimes page is served as plain text only

I've been running a single Drupal site for some time, but recently I added a second site to the same code base (separate database). Since then, periodically, the first site will start loading only as plain text. The CSS and JS doesn't load, so blocks don't appear. There's only the front page text and the home page logo and title. I've found that if I clear the Drupal caches then that fixes it, at least for about a day.

Since my site does not get a ton of traffic I thought I'd add a cron job to clear the caches every day, just as a stopgap measure until I figure out how to fix it correctly. So I made a php file called "clear.php" to with the code below (found at http://drupal.org/node/42055):

<?php
include_once './includes/bootstrap.inc';
drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
drupal_flush_all_caches();
?>

So when this job runs as cron or from the command line (command below) it actually CAUSES the site to go to plain text mode.
/usr/local/bin/php -q /home/user/html/clear.php

If I then clear the caches using the button at /admin/settings/performance or go to www..com/clear.php it fixes it.

Through all of this, the second site is completely unaffected. From the code I assume this would flush the caches for all Drupal databases, not just the one that happened to be installed first. It may be because my default settings.php is setup for the first site. I do have a separate folder for that domain with its own themes and modules that aren't accessible by the 2nd site, so I thought it was no longer reading the default folder.

So I'm at a loss for what to do next. I'm no Drupal expert, so if I've set something up wrong regarding the multiple sites then feel free to advise me on how to fix it.

Thanks!