Extract roms???? So you're using unzipped sets? Well..then you most likely use a wrong scan method.
ClrMamePro accepts:

[rompath]\[setname]\[rom 1 ... rom n] for unzipped files
[rompath]\[setname.zip] for zipped files

I guess GBA roms are one-rom-per-set sets...so if you want to keep them unzipped, you have to create a subfolder for each set.

Roman Scherzer
ClrMamePro