Have you tried to burn the ISO into a CD-R? It works here in 2 different top loaders and in a CDZ.
Viewing post in Street Fighter II Champion Edition for Neo Geo CD comments
Ok, it seems there are some kind of problem with some modded consoles using SD Loader, because I tested the CD-R with non modded consoles (CDZ and top loader) and it works. If you want to help me to find the problem, write me to info@arcadeartisan.com and I can provide you a build with a diagnose tool that can help me find the problem.