Aight, it's like this. I went ahead, created a blank flp and slapped two midi outs in there. You probably should make sure there are NO other generators/samplers/vsti's whatever on board, just a blank document with up to 16 midi outs. I have FL8, I hope you do too, you can download my flp here http://www.terrariumrecords.net/miditest.flp.

Load it up, export as midi, then import into Reason. It adds a bunch of note lanes and stuff but the two channels are loaded into two seperate combinators which you can then assign devices to.

If there are any other problems I can try to help but I rarely ever use midi files so I'm certainly no expert lol. Good luck!!