With the latest updates of TPT, I've noticed a problem with Newtonian Grav: sometimes, after a simulation with newtonian gravity, the deformations of gravity stay even if you reload several times the simulation. It does not happen all the time but it is quite annoying, especially if your doing some fragile stuff. I hope this will be fixed in the next upgrades of TPT.
An easier solution would be to make it so that if Newtonian Gravity is off, gx and gy are never applied to any particles. This should fix the glitch, and also make saves run slightly faster.