Well I finally figured it out completely by accident, though the problem was actually an odd one that seems like a flaw in the system to me (and one I can't understand).
GG wants to save all levels to: C:\Program Files (x86)\Steam\steamapps\common\Game Guru\Files\mapbank, which is where all the demo game fpm files are saved. I created a subfolder in there that I called Tests, where I was putting all the different levels I was practicing in. Because this was my first attempt at something with more than one level I created another subfolder within Tests that I called Multiple. I saved the two levels I was using for my winzone testing into Multiple, within Tests, within the main mapbank folder.
When I gave it another try following DVader's video as mirror step-by-step as possible, I accidentally saved the files into the main mapbank directory this time... and i worked. I deleted the Standalone, copied the two levels into the Tests folder, compiled it, and it worked. Deleted it again and copied them into the Multiple folder. This time it just kept reloading the first level again.
Took a closer look at the standalone's mapbank folder and realized that the maps were saved under:
C:\Users\Owner\Documents\Game Guru Files\My Games\test1\Files\mapbank\Tests\Multiple
instead of :
C:\Users\Owner\Documents\Game Guru Files\My Games\test1\Files\mapbank
Tried it saving under:
C:\Users\Owner\Documents\Game Guru Files\My Games\test1\Files\mapbank\Tests
Still worked
Apparently as soon as the maps I'm working on are saved more than 1 directory away from \mapbank, the program can't seem to find any level but the first