I would suspect that You have an IDE Drive going out, Pos CD,or Zip.. The fact that the system is Booting, and not running IDE Detection all the time would shy me from a CMOS battery, usually just redetects IDE devices on Boot, and works normally. Sounds like when Windows trys to access the device, it locks.. If you have not already figured it out, I would ... Be sure to Unplug, and Ground Youself before opening System.

Unhook the Data Ribbon Cable from the ZIP, reboot, go into BIOS, reset defaults, reboot, and go back into BIOS, see if the CD-ROM shows up. If so then Check the ZIP for problems, if Not then Power down, Unhook the CD-ROM, and Rehook the ZIP, Boot back into BIOS, reset defaults, and reboot, go back into BIOS, check to see if the ZIP is shown.  Do this for each, usually when the problem device is unhooked, and system is rebooted, the working device will show up again. If Both make no Change, Unhook the HD, and try the ZIP and CD then. Have seen a device on the Primary IDE, kill the Sec IDE chain also.. That would be my shot at it..

ZeitGeist