Ive noticed this too, but under a slightly different scenario...

If you have a FW drive or USB drive plugged in when assigning paths, then remove them after shutdown/restart, the drives dont apear in the same order after re-boot, and this is when links to files are lost and do not link to the correct drive again...

Have proved that if you ensure that FW and USB drives are removed before selecting file path in catalyst, then links remain unchanged after a restart etc... not sure how this can be resolved with 2 x SCSI drives though..... It seems to be related to drive order at startup...

Simon