Thanks for the advice. My mame.ini is setup the same way (it has roms;software in the roms path). I did do a fresh install for this Emuloader release so perhaps that may have something to do with it. The software list loading used to work for me on the previous release. The specific error I get in Emuloader is "Error 2: The system cannot find the file specified."
When I add all of the software subfolders to the Emuloader configuration, the error I get appears to be in Mame (the mame64.exe console window shows the error that starts with "Exception at EIP..." while attempting to read memory at "FFFFFFFFFFFF" and then it goes through a stack crawl dumping memory values to the window.