Great news!
Both graphics cards arrived today and so I tried the ISA one first.
Immediately I got a proper image on the screen and was greeted with a BIOS message:
"CMOS battery low"
"CMOS Display type mismatch"
Put in the Necroware RTC module and "battery low" message went away.
Decided to change the video settings one-by-one and see if any made the weird Scorpion graphics card come back to life-
1. Adaptor Shadow Cacheable DISABLED - This was already disabled by default
2. System BIOS Shadow Cacheable DISABLED - This was already disabled by default
3. ISA Video ROM C000,32K ABSENT - This was ENABLED by default, so I set it to DISABLED
I plugged in the old graphics card and now it works!
Also, the "CMOS Display type mismatch" message disappeared using ISA graphics card.
So, all along it was the damn RTC battery. The RTC battery must've run flat and the SBC defaulted to ISA Video ROM C000, 32k ENABLED. This causes garbage on the screen for the old Scorpion graphics cards, but with a normal video card you can get in to the BIOS and make changes.
It still doesn't explain why the 486 SBC worked with the old Scorpion card, but it does. The BIOS looks very similar between the two SBCs, 486 & Pentiums.
Even though one Pentium board is fixed, I still have some work to do though;
1. Fix the second Pentium SBC. After removing the short on the IC with the bent pins, it was working but booting really slowly. I went back to check that IC again and managed to break one leg off. Even with grinding away at the IC body to try and expose some metal, I couldn't solder a wire on. There were some "New, original" ICs available on Aliexpress for £2 each so I've ordered a couple. It's a gamble whether they'll work, but we'll see.
2. I want to replace old HDD with CF card. I have a couple of different CF card caddies and 2.5" to 3.5" IDE adapter.
Does anyone know if a CF card could work without mods?
Next step is to try and auto detect the CF card as a slave and see if I can get it to boot? Actually just done this, it doesn't.
Attached are some photos of the BIOS, video settings and slave CF HDD fail.