I did come across another problem someone was having with their Matrix 1000 and although the symptoms are different to yours the problem could be the same as it involves a bad contact on the ROM chip which could manifest itself in a variety of ways depending on which leg had the problem. I would try this yourself to see if it cures your problem.
>>>>> Here is the posting I found
I recently had a problem with my M-1000. I lost all the sounds in the ROM bank (patches 200 to 999), although the RAM patches (000 to 199) worked perfectly, so I knew that the machine was working okay, and that it had to be a problem with the ROM chip. After roaming the web for answers, a rather helpful chap from Estonia (thanks Margus!) suggested that I open the machine up, use a blade to slightly loosen the ROM chip, and then ease it back in place, being careful not to bend the pins on either side. Apparently, the connectors on the chips have a tendency to corrode slightly with age, and just need a little clearing. Anyway, I did this, and hey presto! I got my ROM sounds back!
[This message has been edited by Nigel (edited 05-11-2009).]