So, when is this information populated?
After the first system start; you'll see the same message on any ACA500plus when you cold-start. If you enter the menu next time (reset with LMB held), it'll show what's already loaded in the MapROM area.
Out of interest, the card was functioning perfectly stable at 42mhz previous to updating it. Is it possible that the update uses "tighter timings" or something and so overclocking that was stable and usable with one firmware may not be stable with another?
A software update cannot change the hardware timings of the ACA500plus. It is NOT FPGA-based, but CPLD-based, and the CPLDs have fixed code, which cannot be changed with a flash update. Only our FPGA products can do that (Indivision, Chameleon and the Catweasel MK4, which was the first to use this kind of architecture).
One thing that may have changed is your power supply's stability, and of course temperature. We've had quite a few hot days in Germany this past week, and heavily overclocking a CPU does require very stable power supply and good ventilation. 42MHz operation may have been on the edge for your card, and with higher temps, your PSU might have lowered it's output voltage enough to become a problem for your CPU.
So the overclocking problems showing up "just now, after the update" is not a causal link, but merely correlation of things happening at (seemingly) the same time.
Also, note that the 28MHz setting is almost as demanding as the 42MHz setting for the CPU. This is because the base clock is 85.12548MHz. To get to 28MHz with whole-number division, you need to divide by 3, but that results in the duty cycle of the clock signal to be 33/66. However, I still added the 28MHz clock rate in order to be able to mimic the speed that the Supra accelerator offered back in the days.
This should explain why you have lost the *two* highest clock rates on this setup. However, it really seems to be on the edge, so you may be successful with a small cooler, new electrolytic caps for your power supply and a fresh voltage setting (yes, many of the original Commodore PSUs have a small potentiometer inside).
Jens