Well, it is not an answer but may help someone help you. I am having the same problem... I use VOID 0.19 and even though I have nothing as a RCS or anything like this I can see by using VOID a acceleration there...I do not know yet where it comes from. By comparision i use some mods that you also use:
mechjeb, AutomatedScienceSampler , Hyperedit , Kerbal Alarm Clock , KerboKatz, station science.
With this the game is pratically impossible to play. Hope someone can solve this problem.