Time Machine wipes previous days when I reboot

I've seen this twice now: when I reboot my 10.6 Mac Pro and log back on, the Time Machine deletes everything but the last backup. I had plenty of room on the external TM drive; I have a feeling what's happening is this. I have 2 internal disks that I do NOT want on time machine. I usually dismount them as soon as I log in and they appear but in the time it takes me to do that, is it possible the TM decides they will need to be backed up and first clears off needed space (which means deleting all of my older backups)? How do I check if this is right, and is it possible to keep those disks from mounting after reboot (without physically taking them out)?