I just started to have the same issue tonight. It started on a pretty standard flight to the Mun, after doing a insertion burn, sprayed from the booster stage, then switched back to the primary vessel, and it was pushing out the Apoapis without any engines running?! Went to Space Center, reloaded the vessel and saw all the parts flying off into the sunset.... I tried loading up a few other vessels, and got the same result of parts flying off. I don't have the tweak scale installed at all, only change I made recently was to install the new auto save mod and some textures for Procedual parts. I will list all my installed mods after this evenings festivities in the morning.