Hi Gmask,
Many tutorials I have followed especially dynamics ones always say freeze transformations before simulating so I guess I have got into a routine doing so for most of my projects probably even when its not needed, I think it gives a feel of the scene being clean for precise calculations or expressions.
Im sure you know when you were learning Maya there was a lot of strange things going on you couldnt answer sometimes and this was one of them for me so I thought I would ask more experienced users.
Cheers