I'm curious, what kind of problems? I see shops do it both ways in my area. In fact, one shop has a pretty elaborate setup where all tanks are submerged whereas another just has large plastic bins and another has nothing.
One of the shops I get fills at puts chlorine (bleach) in their bath water. I left my sidemount rigging on the tanks on when I dropped them off once and the rigging got significantly bleached.
The guys up at cave country told me that filling in water was basically a "wives tale" type thing. Other shops have told me it's important to cool the tanks as has been mentioned in this thread. I'm not sure what to believe really. The shop doing the fill makes that decision, so I guess it doesn't matter much what I think. I'm unlikely to take my tanks somewhere else over the question of fill bath or no.