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I actually continued to have recording problems with Qtractor despite what I said above, but now I have finally figured it out. To summarize: I learned (by RTFM) that my keyboard always outputs midi to channel 1 & 2. When I would record in Qtractor the both midi channels would get recorded into a single track resulting in duplicate midi events. The track would not playback properly due to the duplicated events.

Since my keyboard cannot be configured not to output both 1 & 2 I made a filter with mididings to remove channel 2 (and also remove control 123). Now I can record in Qtractor properly. Here is my mididings filter by the way:

#!/usr/bin/python
from mididings import *
run( Filter(NOTE|CTRL) % ~ChannelFilter(2) >> Filter(CTRL) % ~CtrlFilter(123) )

Sorry for all the noise. Qtractor was not a problem though it does have the feature, as far as I can tell, of combining midi input from all channels into the channel being recorded so one must be aware of this.