On the pool that you are having a problem, did you manually check any of the levels other than full? If you did, anytime this pool is used, the index will go to the Default pool because it is always backed up full, never incremental or differential.
To remedy, either don't check any levels, or if you are trying to do a daily incremental/ weekly full thing, disable the weekly full pool when it's not in use. Pools can be disabled/enabled at the command line using nsradmin.
I have tried reserving specific drives for each pool as gerudman has suggested and it was a fiasco. Legato kept loading tapes labeled for one pool into a drive reserved for another pool. It would then spit it out and reload the same tape, over and over again.
This was some time ago, so that problem may be fixed by now. Test thouroughly...