I had double loops too. I mucked about and found that STP created a separate folder for loops rather than overwrite the Soundtrack loops. Hence you have both ST and STP loops. You can probably delete the folder with the original ST loops. Actually best to move them off to another location and check to make sure you're not losing any loops that might not exist in the new STP folder.
In STP, go into the Search Tab. Click on Setup and you will see where your loops reside, whether they are indexed and whether the check box is checked which determines whether they show up in your Search (list of loops).
I have:
Macintosh HD

ocuments

oundtrack Loops (these are the old ST loops and reports 4112)
Macintosh HD:Library:Audio:Aplle Loops:Apple Loops for Soundtrack Pro (and reports 5211 loops)
Uncheck top box so the ST loops don't appear in STP. Delete them if you're brave.