So you no longer have an accelerator w/ fast ram and you're using that pre-configured Workbench or AmigaSYS install? I'm guessing there's something there that requires fast ram. Or a patch conflict in your User-Startup/startup-sequence looking for something fancier. Holding in CTRL-A A for a few seconds, on most accelerator cards forces the system in 68000 mode. Is that what you're talking about?
AFAIK on a regular, non-accelerated A1200, all CTRL-A A does is resets your system. Holding down both mouse buttons upon startup gets you to the early startup screen. If your computer is no longer booting and have 3.1 installed on the HD, but still doesn't come up, do you see the Kickstart screen at all?
