Do you use Cubase SX?
I know that Cubase SX sometimes sees midiports twice, or just duplicates them. In the Cubase directory there is a folder "Midiport enabler" that contains a file"ignoreportfilter". I'm not exactly sure how this works, but i know that this must be used to filter out certain ports that are listed double. The Cubase help file explains how.
Ik hope you can get the problem fixed. Sorry my help is not very specific, but this was all i could remember about it.