Your description of your problem tells me that you probably did not insulate ALL your frogs.I'd check them all one by one to make sure that there is an insulated joiner at both ends of every frog.You may have forgotten to insulate one or more along the way...it has happened to me and I grew a few gray hairs because of it.This type of problem does occur when you don't check your installation every step at a time...I've done this too.
This failing,I'd check if you haven't accidently crossed one or more of your feeders going to the track.This is also possible (and likely).With DCC,a loco will not change direction when the polarity isn't right but will definitely create a short when it hits the track joint where the polarity change is present.