I don't have a question; I've solved this already. Posting this in case someone searches these terms.
Problem: my SCC CTC+SIO card didn't work when jumpered to use-CTC-for-port A.
It worked fine when port A directly used a clock, but I wanted to have software-adjustable baud rates (I have a real terminal that requires specific rates).
Exploring, I found that it worked fine for CTC-for-port-B ("baud $2 $96", "console 2" switched to using port B at 9600 baud).
I assumed this was a hardware problem and scoured the board for bad soldering and swapped out a CTC and SIO/2 for known good ones; none of this changed anything.
Digging into the software (SCMonitor/Source/Config/config_S8_SC150_151.asm), I found that it disallows SIO+CTC for port A, apparently as a compatibility thing for SC110. I don't have a SC110 (I'm using the later RCBus-design), so not sure what the problem was/is about.
However, commenting out this line in the that file, assembling, and reflashing the chip works:
kSIO1ACTC: .SET 0 ;Port A's CTC register (0 if n/a)
The file says that this line was needed for SC110 port A to work correctly, but on my later board, it works now using the CTC.
Anyway, nothing to see here. Just a note to a future person to save them some hardware debugging.