CJ, are you using an (E)ISA I/O card to get your ports? If so, does Windows recognise it? If so are you using a driver? If so I'd love to get my hands on it!
I want to run two floppies and have a card last known to be working on a 386 with Windows Ver 3.1 that has the Serial and Parallel connectors and the FDC but it can't be seen by my W2K.
Modern MoBos have a single FDC on the board.