This is perhaps the worst possible time for Flores to slump. Manny Acta has shown that he doesn't need reason to make stupid decisions, but a slump makes it even more likely that we'll soon see Lo Duca back at the #2 spot.
Flores shouldn't be batting clean-up regardless. Too much pressure for a 23-year old basically rookie catcher.
No reason to worry too much though. You just couldn't expect Flores to keep producing at the ridiculous level that he was for such a long time.