Hi everybody, i'm experiencing the same issue on low Kerbin orbit trying to build a space station. I placed the first two modules in a 80km stable orbit with some difficults because the first module already changed his orbit a little bit, but when i got there with the third one the station's AP was 84km and PE 70km.
I docked and watched what happened next: even with no engines (modules have only RCS that i disabled as i did for SAS) the station continues to slowly accelerating, yes, not slowing but accelerating.
I placed other 3 SATCOM at a geostationary orbit but they don't seem to be affected by this bug.
Hope they fix this as soon as possible..