I have kind of the same problem. Some 2,5m parts (MK1-2 Command Pod, Rockomax Brand Adapter or Rockomax Brand Adapter 02 for example) shift the center of lift of my rocket to one side. Tanks, engines and other 2,5m parts on the other hand are working fine. I tried it with FAR and NEAR with the same result. Does anyone have an idea what could cause this or has a solution? Would be much appreciated.