I think low ceilings generally have poor acoustics. This becomes worse when both the floor and the ceiling and floor are relatively smooth. Just about any smooth surface will cause your sound guy fits. I think what you're hearing in the toms is going on with everything on stage. The toms are just sounding worse than anything else to your ear. I could be wrong though.
I was recently invited to a party at a rented community center / pavilion building. It had a peaked ceiling but the walls, floors and ceilings were smooth. The band was very good, but the acoustics were crap. We actually had to go outside to hear the band better. It was also very loud and boomy.