Hmmm... My understanding was that two of the buttons on the CD32 corresponded to the left and right mouse buttons, i.e. were simple on or off, wired directly to the LMB and RMB pins on the port, and the last remaining pin was used to switch to multi-button mode where the rest of the buttons could be read. If you plug a mouse into the port and press the buttons does it behave like two buttons? You could also try a Megadrive / Genesis controller which followed almost the same pin configuration, so two of the buttons would work on the Amiga.
