I'll second worms. Based on similar symptoms in both dogs, and the fact that they are fairly recent off the track. It's not unusual at all to have worms show after adopting, even though many groups give a de-wormer right off the hauler. It often takes multiple tries to get rid of them completely.
There have been several times that we suspected worms and had a negative fecal. We treated for worms with Panacur, and the issue went away. The only thing a negative fecal really means is that the stool that was tested didn't have any. It doesn't mean they aren't there.
The only other thing I can think of is gas pains, but if you aren't hearing some squealing from the belly, it most likely isn't gas. If you suspect gas, you can try giving 1 regular Gas-X tablet (not the kind with extra antacids etc.)