How is the G3 upgrade installed physically? I recall I removed my stock 601 card from the 7500 to exchange it for a 604 upgrade.

So my 7500 only had one cpu to boot from. For the Centris650 I had a 601 cpu upgrade to be installed in addition to the 68040.

Therefore it came with a init/control panel to select the cpu at cold start.

Could it be you are missing some kind of software to select the cpu, as you seem to have installed 601 and G3?

Otherwise it may be the PRAM battery beeing weak, so your Mac will default to the stock 601 at cold boot.