Have you disabled 1 of the IDE channels provided by the VIA chipset (eg. only Primary IDE enabled)?
If so, Windows usually doesn't pick up that properly and tries to load drivers for both. The way around it is to go into Control Panel->System, bring up the device list and select hard-disk controllers.
In this part of the tree will be 'VIA Bus Master PCI IDE controller' (or something similar). Double-click it and select the 'settings' tab, and then select in the drop-down list the correct configuration (as in the BIOS) of the IDE channels.