Discussions about Winboard/Xboard. News about engines or programs to use with these GUIs (e.g. tournament managers or adapters) belong in this sub forum.
You are absolutely right. The code made no provision for pondering at all. (As node-based matches between engines often have time-odds character, pondering might defeat the purpose.) Pondering even wrecked operation in Two-Machines mode, for which NPS play was meant.
I put in code now to test if the engine producing the Thinking Output is indeed on move or not. Thanks for spotting it, and pinpointing the cause.