Maybe you limited the number of sets....(checkbox should be checked left beside the name in the set information window).
I've just tested it with a profile based on the single hash file and scanning and rebuilding works fine, also in full software list mode it works fine.
So...question is how you set the profile up....what you can do is to
create a new profile based on the single aim65_cart.xml file (so all sets are enabled by default), setup a new rompath for it in settings, switch to full merge mode and rebuild...everything valid found in the source will be added to the destination...
So...if a new scan does not list anything missing your setup is different...either you 1) limited the number of sets or 2) scan different data or 3) use multiple rompaths so parts come from path 1, others from 2....
All I can say for now is: it works fine....To help you I'd need more information about your specific profile setup
or turn on rebuilder logging (in rebuilder advanced) and check what is logged or post it here