[Dr.Einstein]

Here is what you do. Download the crashdetect plugin and use it. It will help you a lot., as it was mentioned above.

What I can say about this, it really sounds like an array index out of bounds which can crash the entire server. This used to happen to me back in the day. It must be an array somewhere in heart of the script.

If else fails, create a debugging system.. printing a message after each line that you suspect the bug is at.