I figured out why this issue happens. Apparently using the files posted online for higher resolutions, giving 10 or 15 saves, and fixing cinematics is why the CD 3 error happens (those files are technically altered from the Spanish version or English Demo version). But, I found a way to fix it without having to start over.
Fix: Once you get to the place where it wants CD 3, you need to revert back to the original GOG version of alone4.exe (the modded launcher.exe file does not matter). The problem you will face if you have the altered save version of the exe with 10 to 15 spots is that it will show you have no saved games when returning to the original exe. That's because the extended save exe makes a folder for its save files, but the standard exe just saves them to the parent folder along with alone4.exe. You just need to move your last 5 saved games from the Save folder over to the parent folder and rename them ending in 000, 001, etc. up to 004 (unless you have the quicksave which counts as one of the five). You can then resume your game as normal. I think just sticking to the original alone4.exe and use the altered launcher is probably the way to go from the start so you don't run into this problem half-way through.
Post edited October 16, 2022 by dacripe