(edited)
originally i wasn't using the 'MalaGamelist.exe' in a way to make this work for me, i'll explain below. my misinterpretation was pre-sorting my ROMs and while MaLa was running check marking the ROMs option to choose only the ROMs found in my rom folder and hope it would also read the different clones of the parents.
here's what i did to resolve this dilemma:
- created a ROM project list, including the proper revisions / versions desired (text file)
- loaded MaLa, right clicked, options, rom path options, unchecked everything, allowed MaLa to do what it needed to do then closed MaLa
- put 'MalaGamelist.exe' in the MaLa.exe root directory and executed the file
- at this point i have all 7,200+ MAME games in the list and began adding the games / versions / revisions desired while referring to my text file. i also took this time to rename a few as needed. i saved this list as 'Favorites.mlg' in the MaLa.exe root.
- opened MaLa, right click for the options pane, chose my newly created 'Favorites' list
- now all is well and good

Thanks for getting me to rethink the use of MalaGamelist.exe!
btw, is there a way to reorder the games in the list? they seem to be auto sorted alphabetically.
thanks!!