Bose sound - am I going nuts?

[Jaxonalden]

If you don't mind my $.02 worth. You say the "Bose" system, unless all the system signals go through the amp in the front truck I don't think you can blame Bose. I'm sure some speakers are powered through the radio itself and if that's the case you problem is with the radio and not the Bose system.
I just checked my Bentley manual and the wiring diagram shows all wiring for the speakers, with the Bose system, run through the amp. So it's safe to assume that the amp is somehow overheating and tripping a thermal fuse. Once the fuse cools and resets the speakers are powered again.
Check to insure you don't have anything laying on or around the amp that might impede cooling air from circulating around it.