Sorry, I should have clarified-- the screenshot was only meant to illustrate the title line. Here's how things look when everything is "OK":


The title line shows 14029/14029 when Select All is clicked (also by default) and shows the Namco sets as selected when "%I=1" is applied. The title line then reads 12/14029, as I would expect. Like this the Namco sets are able to be scanned and rebuilt as usual.
Here's an additional picture to clarify the one in my initial post:

Even though "%I=1" is applied and the proper sets are selected the title bar now shows 0/14027 (not 14029) and any attempts to scan or rebuild the affected sets fail to list them-- they appear to be ignored.
Here are two additional pictures showing the same thing happening with MESS:


I'm not sure which sets are affected when it comes to MESS but I suspect it is related.
I've replicated this with two different binaries of MAME 0.143u4, one I compiled myself and another I got elsewhere. The pictures here were taken with both MESS and MAME at 0.143u5, each build being 64-bit. When creating the MAME profile I always answer Ok to All/No to All/No to All. I was initially reluctant to post this because it's entirely possible that this is all on my end. What nags at me is that even though it appears to be semi-random, only two distinct cases are ever the result and the same sets are affected each time. I'll see if I can narrow it down some more.