Please help!

All of a sudden my Cubase artist 6 on my production PC has gone haywire on me! I use an Alesis Master control and the combo has worked perfectly. I had to disconnect the controller due to an evacuation order, and when I plugged it in again yesterday, all of a sudden this happens :
I can’t control track 1-8, only 9-32! The bank button simply will not go to bank 1-8. neither will the track button. If I add 32 tracks, so that I have 40 track, and delete 1-8, the controller will only control track 17-40! No matter what I do, the first 8 tracks are “out of range” for the controller. Furthermore, if I open the Mixer window, the highlighted track in the mixer window, is not “mirrored” in the project window. So for ex. track 2 may be highlighted in the project w. while, let’s say track 7 is high lighted in the mixer window! The touch sensitive faders will select tracks in the mixer win. (or at least track 9-40!) but not in the project window!
I have tried everything, re-loaded the Alesis driver, and even removed and re-installed Cubase, but to no avail. I was ready to send the Alesis in for repair, assuming that it was the culprit, but first I downloaded Cubase 7 trial version on a whim, and everything works perfectly in that program! So the master controller is not at fault, obviously. Furthermore, I unplugged the Master controller to see if the mixer/project window “mirroring” problem was dependent on that, but no, it does the same thing, master controller or not. On my laptop the program works fine!
Does anyone have any idea what is going on??

Go to Devices, Device Setup. Under Remote Control Devices, what do you have listed? I would suggest removing from there and adding the Master Control back in (I would suggest contacting Alesis to see if they prefer Mackie Control or HUI). Then reconnect the MIDI ports accordingly.