I've had 1 cherry barb end up on the floor, and a couple of crabs and a couple of shrimp, but still think open top is nice. I've been playing with partially closed tops to reduce evaporation, but find it blocks a lot of light.
What are you using for covers? Plywood windows? [/sarcasm]
I had a plastic cover for my 12g when I had it set up in Korea...and water would condensate on it like crazy and drip back into the tank. I found that there would also be some sort of deposits left on the cover after a few days, and the longer it was there, the worse it got...though those stains never seemed to do worse then a poor diffuser for my lights (it looked like salt stains). If this is your problem, you may need to take off your clear plexi/glass covers and wipe them with a vinegar mix as part of a monthly maintenance cycle...though I found plain water and a rag worked well for me. If the tank weren't covered, I figure I'd lose about an inch of water a week...not that big of a deal on a 12g, but still annoying.