[Kerbal Space Program update 1.1 “Turbo Charged” is now available!]

My tests seem to support your part clipping theory. I took the same probe and put normal sized fuel tanks and engines on it and it behaved normally. I also tried removing the re-sized parts and replacing them with "new" instances of the same parts, just re-sized while using KSP 1.1 and they also behaved normally.

[Kerbal Space Program update 1.1 “Turbo Charged” is now available!]

Hmm... Could be. I generated an instance of one of my satellites and put it on the launch pad to see if it would explode. I did not explode, but it did twitch and rotate like it was experiencing some phantom forces. It did not have SAS on and even it it did the probe is too heavy to be stabilized at 1G. It should have just fallen over. I used tweek scale on the fuel tank to make it smaller, so maybe that is the cause. I'll have to see if that changes the behavior.   

[Kerbal Space Program update 1.1 “Turbo Charged” is now available!]

I am having some of my pre-existing, launched  ships explode to various degrees and get propelled out of orbit. I haven't seen it happen to any of my test ships since the upgrade. Any suggestions?