Youre doing it wrong. Lol!
If I had to guess, you ned to change your command-line from:
C:/HiScore Updater/HiScoreUpdater.exe" -type 0 -mappath "C:/GameEx/Map Files/HiScore Competition.map
To:
C:/HiScore Updater/HiScoreUpdater.exe" -type 1 -fpath "C:/GameEx/Favorites/HiScore Competition.ini"
Change the favorites path to match your current setup, or where you save the favorites file to.
Compiling MAME will not make any changes (other than the options you compile with), all a custom compile does is add extra functionality, such as removing the nag screen, adding high score functionality, and adding Direct Input instead of Raw Input. If your artwork is being distorted, thats more likely because of using DirectDraw.instead of Direct3D.