I believe I fixed the issue.
It turns out that I wasn't using Rosegarden properly. So it wasn't a bug in PB.
Don't change anything in the "Track Parameters" section of Rosegarden. I was changing the instrument here when I should have been changing it in the Bank/Program section under "Instrument Parameters" Changing the Instrument in the "Track Parameters" also messes with the channel and you won't know until you save it and reopen the file.(Maybe a bug in RG?)
My problem is that when I set the RH and LH parts as piano, RG made both parts channel 1. I didn't notice until I woke up and reopened the file. This is also why PB said channel 11 when I wanted Instrument 11.
For most music, all you need to mess with is the "Program" and "Channel Out" in the "Instrument Parameters" section and Ignore the other sections.
The version of RG I was using was 1:1.7.3-1ubuntu1 64bit
The source for RG (if you still want it) is here
http://packages.ubuntu.com/karmic/rosegardenYou can download it on the right.
I use the "Notation Editor" in Rosegarden and then "Step Recording" which allows me to input the notes from my keyboard. I then export to Midi under "File->Export->Export Midi file..." This makes it pretty easy and quick.
I am attaching the midi file and the RG file to help those who want to use Rosegarden to make their midi files for PianoBooster.
PianoBoosterTest2.midPianoBoosterTest2.rg