Midi File import and enharmonics

I'm starting to experiment with MIDI file input. It looks to work pretty well as long as I massage the MIDI first. But the way to import a MIDI file seems to be to open it as a file. And at that point a key signature has not been established, so many notes can be enharmonically incorrect. Changing the key signature does not seem to reinterpret those notes correctly in the new key signature. I'm sure there must be a way to deal with this but I don't know what it is.

Any help would be appreciated.