TJ -- I have a STRONG suspicion that your entire problem will be solved if you disconnect your cdrom drive's ide cable, set your dvd drive to master, and use the dvd drive for all cd and dvd-related functions. (i.e. disable your cdrom drive all together)
Sounds to me like your computer/bios/drives/etc. are having a hard time playing nice together on the same ide channel. Though this would put more wear and tear on your dvd drive, with prices dropping so low for these, IMHO, that's not a big deal.