Okay, solved and this is one I recommend making more clear in the documentation. My issue was that I ALWAYS keep a wireless keyboard connected to my Retropie. It's just a tiny dongle taking one port so why not? It's so much easier for certain tasks.
However, I kept wondering why the test rom for Intellivision was reporting that I was on controller 2 and every other comment pointed to controller one. Then I noticed posts where people said that Daphne and Intellivion (jzintv anyway) assign the first controller they see, which in this case was the keyboard -- and that explained why the keyboard worked. Ugh.
I sent back and took a CLOSE look at emulators.cfg (where you add the link to the hack file) as I found it odd that mine was already there.
What I realized is that it was there, but for the tzintvecs (which I assume has something to do with running things in the expansion port). So, I added it to the main program as you can see below, but still nothing. Changing the JS1's to JS0's also made no difference after this fix.
@Unknown I made the same mistake when I first started looking into building my first Retropie then remembered that the NeoGeo home console (AES) was essentially the same hardware as the arcade unit (MVS) but could only have one cartridge as opposed to the up to six cartridges of the cabinet.
If there is no /opt/retropie/emulators/jzintv folder after installation, then it means the installation didn't complete correctly. Note that the install doesn't add a hackfile, so if your configuration included one, you'll have to add it manually.
I think quicksilver may have found your issue as your BIOS files should be in /home/pi/RetroPie/BIOS/ and your setup appears to want them in your roms folder. You could try copying them there if they are not already and see if it works. My Intellivision retroarch.cfg just points to the global one in /opt/retropie/configs/all/retroarch.cfg I dont have any custom values in it other than the input remapping (maybe you have something else?) in the global file you should have system_directory = "~/RetroPie/BIOS"
Lowercase, in the BIOS folder.
[EDIT: actually, it was Exec.bin.... for some damn reason the first letter was capitalized and even as I replaced it with other versions all in lowercase, it kept the first letter capitalized. I deleted and replaced it with an all lowercase exec.bin and it works now! Thanks so much!]