thanks for theresponses. I had this setup many years ago and had it working fine. I revisited a old setup. I realized I did had a system linked to "SNK Neo Geo" at some point. Anyway I revisted my setup. The main menu xml does have to do with sync as you set link to the available systems to what you have in listed listed in the main menu xml. I have added and removed many systems prior with no issues. I just forgot some minor details as it had been a while. I added new and deleted systems to re familiarized myself. From this exercise if added, I could link to that system and if deleted I couldn't link as expected. I noticed when I "dropped" a system from the media configuration section, the sync systems would also update. Likewise, if I added and set link to a system that wasn't listed before in sync system section it would update. So this answered my question I posted in thread originally in regards to how the sync systems were populated. Feel silly not seeing this before.
Within reason I came to conclsion I mustve done some wrong or didnt drop the snk neo geo system way back when and it was still listed as a available system and caused a mistmatch. I located ini files where hypersync stores settings. Within the settings ini file, all systems I had setup were listed. The odd ball was "SNK Neo Geo", which I had no use for since nothing was linked to it via my setup (Sanity checked and went through all systems and verified nothing was inadvertantly linked some how). "SNK Neo Geo" show it was linkd to "linked=SNK Neo Geo". I just removed the system from the systems ini file. Problem solve. Restarted Hypersync and everything worked as expected. Annoying this happened but I it helped me recalls some things I had forgotten.
I don't hand edit xmls by the way. I only use xml from hyperlist.
Anyway, I apprecaite the help and responses. This is a non issue now as I have resolved. Added some screen shots for clarity just in case.