Baffling Problem - Site Crashes

[eluser]Unknown[/eluser]
One of our many CodeIgniter sites is exhibiting extremely odd behavior. It is hosted on shared server using a fairly standard LAMP setup; SuSe Enterprise, Apache 2.?, PHP 5.3.8, MySQL 5.1.70 enterprise. We're using
CodeIgniter version 2.1.3.

Several times per week the site just completely stops working. The database is still up and running. Apache is fine. Other sites (including other CI sites) on the same server are up and running. But this one site just stops responding. We've tried restarting Apache, restarting the server, etc. but neither of these actions fix the site. The only thing that will get the site back up is to delete all of the files in the root directory and re-upload them. We've done diffs between the old files vs. the new files but they're identical.

There are a few things that are different with this site than the others:

-- We use CodeIgniter's caching functionality for this site. This is the first time we've used it. It seems to work well. It certainly speeds up the site.
-- We use JQuery extensively throughout the site. Specifically, we use a lot of AJAX. We've seen the posts regarding session issues when using lots of AJAX (https://degreesofzero.com/article/55, http://stackoverflow.com/questions/79801...ajax-calls, http://www.hiretheworld.com/blog/tech-bl...conditions). We have even applied the suggested fix but we're still having the problem.

These are, of course, the first things we looked at when trouble-shooting, but nothing we do seems to help. We've been dealing with this issue for months. We're getting desperate. Does anyone have any suggestions? Has anyone seen behavior like this previously?

Thanks in advance for you help and suggestions.

[eluser]CroNiX[/eluser]
Is there anything in the php error logs, apache logs, or CI error logs?

Could this be a permission issue? Owner gets changed somehow? The files might be the same but the diff won't show anything different if it's a permission issue as that has nothing to do with the file contents.

What happens when you visit the site when it's in this state? Error messages, blank screen, etc?

Sorry, just throwing ideas out there.

[eluser]Unknown[/eluser]
CroNiX,

No reason to apologize...I appreciate the input.

We've definitely consulted all logs and have never found any smoking gun.

A user would see a blank screen when the site is in this state. Sometimes you might get a generic error from the browser (depending on which browser), but nothing that helps us troubleshoot.

We've definitely considered that there might be a permission issue, but we've investigated this and haven't found any obvious issues. Further, we've reset all permissions on all files when this happens but to no avail.

Note that we do a pretty good job of keeping these systems patched and up to date, although we are certainly not early adopters. FWIW, there is some evidence that these issues started when we upgraded from php 5.2 to 5.3.

Also Note that this site is internal so it shouldn't be subject to any outside issues (but I would never say never).