I don't think it's a permission problem as I can see the files in Windows so ClrMAME should also be able to access them, should'nt it?
This results in the following error:
info using already existing xml export
info loading: C:\Users\Charel\Desktop\clrmame\exports\bc03e79e-listxml.xml
info building split view, rebuilder map and destination patterns
info 47966 split merged machines selected
info rebuild start
info analyzing rebuilder source: Y:\MAME\ROMs, please be patient
error analyzing rebuilder source Y:\MAME\ROMs failed due to recursive_directory_iterator::recursive_directory_iterator: Invalid Signature.: "Y:\MAME\ROMs"
info thread pool size: 10
info analyzing rebuilder destination: Y:\MAME\Fix, please be patient
info optimizing
info finalizing and cleaning up
info rebuild end, took 0 seconds
info Done, overall time: 12 seconds
error errors occurred, please check log
Could the fact that the MAME executable is a level lower than the ROMs folder (as you can see in the config) be the source of the problem?