Hey Michael!
I had to switch it back to SuPHP.
Yes, it is a mod_fcgid bug, because the only way to increase the FCGID_MAX_APPLICATION is to editting the source and compile it again. There is just one bug report to this and no much information.
It starts to happen when you have more than 1000 applications for an user.
Everything will be normal, until the limit is hit.
So, at this time, I had no other option, unless to switch back to suphp and prefork.