Surprisingly found the same issue still happening in the latest release
Following my issue here:
https://www.emulab.it/forum/index.php?topic=5273.msg21178#msg21178My observation from the behavior of clrmamepro concludes that: the scanner/rebuilder does not seriously treat the manually assigned system ROM paths for software-lists, and implicitly assign a destination path unexpected by the user.
In my case, the rebuilder undesirably creates software-listed roms in $mameroot\software instead of $mameroot\software\$mycustomed_system_path, and when the scanner does the checking, the created roms are deemed as "misplaced", generating a significant amount of error messages without the capability to move them to the correct place.
I am not sure if it is technically hard to add some intellegence in defining the rom paths.