Crap... I didn't boil the water before topping off the carboy. I did use filtered water though. Wonder if that matters.
Thanks everyone for your responses. They were really helpful. Next batch I'll keep it in the primary and skip the secondary. Being new to homebrewing I was excited to be more involved with the process but I'm now realizing I'll need to be more patient and let the beer do its thing.
Speaking of impatience - I'm anxious to try an all grain brew. I've been reading a lot about brew in a bag. I have a couple 6 gallon pots so was thinking of trying the two pot method. Anyone have any personal experience with this method? My only concern at this point is low efficiency.