RCS Question/Problem with Space Planes

Has anyone seen this? I've designed several space plane/shuttle type craft. Once launched into space, the RCS either doesn't function at all or the controls are all messed up. Example: I push "E" to roll right or I push my "2" button on game controller. The craft should roll right, but either it doesn't move or it pitches up/down or rolls left. Sometimes I get a combination pitch and roll. I see the wing control surfaces move as they should in atmospheric flight but they shouldn't have any effect. I have tried both the RCS pods and RCS "circle thingies". Once back in atmospheric flight, axis control is normal. I've only seen this since the last updates.