:pint: Hello, Brian, and welcome to Amiga.org!
:-( As to your situation, nothing obvious springs to mind.
My first suspect would be Degrader, since it is able to do things like that. (sixteen colors was the maximum for high-res, OCS and ECS miggies.) Also, there is an option in the early-startup menu to fall back to the OCS and ECS chipsets.
:-? Is there something in your WBStartup, or Startup-sequence or User-startup that calls Degrader, maybe?