Looks like a problem with the rewrite engine, not the problem I mentioned.
Can you please turn on the rewrite logging under the "Rewrite" tab? And send me the log messages for a request that results in 404 code (with the file not found error), grep with the client ip address can be used to find relevant log messages.
Looks like the rewrite rule has not been executed for the some request.
You can also try moving the rewrite rule form .htaccess to the vhost level.