Well, the globals are being overwritten because the compiler is somehow mistaking a local variable (array - msgBuf) for a global one. It happens to be caught early, because userFont gets blown away too and Print needs this.
PART 2:
That was SCI0. Now in SCI01, this problem doesn't occur. Instead, the conductor filename is somehow bugged. The default name contains a backslash, and I've never had to use one before in SCI code. The backslash causes SCI to create a file named MMAND.CON instead of COMMAND.CON. You could sidestep this problem entirely by running SciAudio and SCI from the same directory, or you could try to figure out how backslashes work in Companion's string handling code. Or do it on the ScIAudio daemon side of things (command line?).