I/O Operation Failed - Server Down

We are having a dedicated server with Windows 2003 and Hosting Controller on it with MS SQL 2005 Express Edition.

Since last few days, we had this problem that MDaemon mail server would go down on some pagefault and server used to get hang, and when we investigated Event Viewer, we find 100s of errors of the following message.

Quote:

An I/O operation initiated by the Registry failed unrecoverably. The Registry could not read in, or write out, or flush, one of the files that contain the system's image of the Registry

We replaced HDD, and reinstalled windows 2003 and built the server back with every peice of software we had it earlier, but now the old HDD is still there as D drive, but not in use, still server got down today. We belive its no longer the HDD issue, but now problem is how to get root of this problem and how to monitor?

I had minor hint from searching on google that some trojan would create too many handles would cause system to go down this way, but here we rebuilt the entire server with fresh installations downloaded from vendors websites.

If MDaemon is creating too many handles, how to monitor and how to restart it in such an event?