I'm also having reentry problems. Not sure if it's a bug or working as intended. I assume with the new physics engine this is all working as intended.
My reentry capsules seem to be coming in with much more velocity.
I was having the issue you're having only with goo canisters blowing off. The solution was to put them in a parts bay underneath the craft. Haven't had problems with the parts bay or a science junior under my reentry capsule though. I have had problems aerobraking larger reentry capsules... velocity at about 1000 meters is just above parachute threshold.
