I have both MBAM and SuperAntiSpyware installed and I don't have any problems (but only one can be resident), However, Spybot S&D has been a problem at times with its resident protection blocking new start-up entries, but I don't think it would present itself in the way you describe.
Personally with avast (which incorporates anti-spyware detection) and MBAM there is a question if you even need S&D, plus S&D used to be really good years ago, it isn't in the top flight right now. So at the very least disable its resident protection or uninstall it.