I too am having this issue. Also scaled parts seem to wander when loading into the world (VAB or flight). Try loading a craft several times and see if the part starts to appear in an odd location. Had 4 tanks foating several meters from my lander because I had moved them to overlap the center tank. Each load they moved a small amount outward until I was left with a VERY stable yet VERY impossible lander.
You are the first I've seen with this same issue. Hopefully Lisias can give us a fix. KSP is an addiction and it isn't the same without tweakable parts.
