One issue I've had with covering is the small pockets of water that you often get on the cover, which don't circulate.
I ended up with an algae bloom after taking off the cover, and not having sufficient chlorine in the rest of the pool (was only FC of 3, CYA 60, which isn't TOO bad). My suspicion that I can't prove is the pockets of water gave the algae a chance to get established, then it spread when I took the cover off.
If I ever use the cover for a long period away again (which will keep the FC in the whole pool higher), I might bump my FC up higher before taking the cover off to prevent that.