Well...First I kept calling the board C03 when it was actually S03 for the R4LC board originally in the engine. And the one I had in stock that kept the engine from taking off by it self is an R4LC S08-S01 board. And I am pretty convinced that the S08-S01 board is different enough not to run this legacy engine throttle wise.
I was checking out the signals on the R4LC S03 board (Rigol scope, eh?) while the engine was running by itself and it appears that the forward and reverse lines out of the board were low mostly with an occasional high pulse or two. Plus there was a lot of noise on +5 and some on other pins. I was using the ground on the heat sink to refer the scope to. Checking the continuity of the ground pins to the outside rail, I got a lot of intermittent resistance. So I suspected a ground issue on the board or engine to be the source of all the problems.
BUT WHILE I WAS CHECKING THINGS...the engine started functioning properly. With the S03 board. Before it fixed itself I tried the S08-S01 board and it still didn't allow me to run the engine with the throttle and the signals out of the forward and reverse pins were high...and the engine did not fault to running by itself. So the ground issue seems to have been on the R4LC S03 board and not in the engine. The mother board seems not to have been the issue since I have had the boards on and off a dozen times without any change in how it behaved with either board. I cannot find any solder joints on the board that look suspicious...no hair line cracks around the pins, etc. The fact that the forward and reverse pins with the S08-S01 board stayed high and the engine never faulted ever with it (even though it would not run with the throttle) makes me pretty sure that the S03 board has, or rather had, the ground issue.
I think the best thing to do here is return the engine to service (belongs to one of the train running friends in our somewhat informal club...I seem to be the guy they say "could you look at this". I say "no time", but I do it anyway and work free trying to avoid starting a new career), and order an R4LC S03 board for stock.
Thanks to all for your patience in reading this, hope it adds to the knowledge base, and thanks for all the comments.