Created a duplicate of my MAME folder and experimented.....
First, I created a new MAME datfile, importing softlists. Second, I made a second roms folder in my MAME directory and moved the console game subfolders to it, leaving everything else as it was. I then added each console subfolder to the rom paths settings in clrmame.
With this configuration, clr runs as expected. I still don't understand why its such a problem for those subfolders to be in the roms directory, but whatever works I guess....
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