Hi Matt,
I am ripping audio (to FLAC). I've tried ripping from the specific drive as you suggested, but it's still trying to access drive R: rather than S:
I've also tried playing a CD from drive S:, and again it tries to access drive R: instead.
It's not a general problem, as I've just successfully played the CD in drive S: via iTunes.
Wacky question...
Are the drives in question Parallel ATA drives (with the ribbon cable). Many, many, many years ago, I had some wackiness with my optical drives (when using two drives) and it turned out I had one of the two drives Jumpered to Slave mode (on the jumpers), but physically connected via a non-shared cable (no other drive was on the same ATA cable).
It would work fine some places, but mess up in others (including MC, but also my CD burning applications at the time, it turned out). This was forever ago, and doesn't apply at all to SATA drives, but it is worth checking, since you have two drives...