More strangeness…
Without doing anything except trying again, it seemed to work. That is, until I switched the B machine program, and again, B disappears, and I'm locked out from using it.
The same phenomenon occurs when the unit is clocked internally to 44.100 KHz.
Perhaps an internal clock issue? Oh man, I have a sinking feeling that I'm really going to have to send it in for repair. 
You should also know that months back I tried to describe a similar issue to support. The symptoms were a bit different, but the result of not having two machines available was the same. I reloaded v5.3 over the factory shipped 5.3 OS and it worked better for a while, but this new issue seems to have taken it's place. Previously I never saw any message at all, but was also unable to edit any currently loaded program because the effect would change to an awful sound. It appears to be that this strange annoyance has been with this unit since I bought it.
I hope this helps narrow down things. Please let me know how to proceed.
