Hi,
An unusual problem and not one I've seen on here before. Server 2003/XP had this problem quite some time ago, but it was corrected with an update.
This can be caused by CRC errors causing the driver to reduce it's communication speed.
Could you RDP into the server, and check that your Atapi.sys is dated, or later than this version: 23-Apr-2003 16:29 5.1.2600.1211 If your using the original drivers, it could be installing older versions. It could be worthwhile checking if there are up-to-date versions available.
The other idea is, do you have a DVD drive in the unit? It could be an older type which is PIO mode only. If so, after running for a few times, the drivers might get confused,and reduce all drives to the lowest common denominator.
It could be worthwhile unplugging it and trying without that.
Colin