Hey there, I recently had this happen to me almost exactly as you described, especially with emulated games, and it was because the file name was too long, even though it was the default file name from the creators, usually they were long titles with a sub title that stretched the name past the character or text limit. It might be fine for windows, but the xbox had a smaller file title character limit than your desktop PC. If you rename the files to shorter names, usually it will work. However, changing the names also could change the file itself from working, in my case it was Bin and cue files for a ps1 emulator. In my case, I had to open the Cue file in notepad, and manually change the code and replace the bin file name to the new changed name, and everything worked just fine. I am almost positive this is what is causing your issue.
Cheers!