We have used a GUI for 5x5 chess. Indeed, promotions may occur in "wrong" ranks. It is a patch for ScidvsPC, and it is not very clean. If you want to use the Gardnerfish engine for some reason you need to load a fen or a pgn file before lauching the engine.
The latest code is available from subversion: svn checkout http://svn.code.sf.net/p/scidvspc/code/ scidvspc-code