Dan, are you running from external or internal, or split install? For me, when I double click on a sgu/mgu in Explorer it'll open BIAB the first time, but subsequently it'll open in the same bbw64 process. I personally just opened half a dozen files sequentially by double clicking them in Explorer, and there is still only one process related to BIAB - my thought is that on your computer the files are associated with a different bbw executable than the one you're running initially, or perhaps mgu and sgu are associated to different exe's.
Wow, did not expect that. Ok, first let me confirm for you that every time I double click on a BIAB file it opens a new unique version of the program. In the image below I illustrate this with three files. This has always been the case for me (best I know). Regarding why this happens will take a little time. I will look close at what you are suggesting.