You'll have to crack the manual to figure this out exactly, but it is because the QS has a strange way of sending midi data. In Mix mode, it sends data out on the channels of the individual patches being played. For example, you are playing a piano/bass patch. If you check it out, the bass (below say C4 is on channel 2 and the piano, above C4 is on channel 1 [I know you could also get this type of sound with an individual patch, but let's assume it is a performance]). Well, if I understand it correctly, QS is sending out channel 1 data above C4 and channel 2 data below C4.
There are a couple of fixes. In some sequencers (Cakewalk for example) you can set the channel to record on "midi-omni" meaning it will record any midi data. If you recorded it that way and checked the individual notes, you should find that some were sent on channel 1 and others on channel 2. Or by going to edit/global then paging to to page 6 "KBD Mode" It is probably set to normal. What I do to record midi data is play something in patch mode and set the Kbd Mode page to output on channel 1.
While it seems a cumbersome system to me, I think Alesis' reasoning was that if you wanted to set other modules up (using the QS as a master controller in a live rig), it would be easier to configure them.
Hope that helps.
