I think you guys may be right. It's just odd that it only happens when I attempt the glitch.

No :p The first half I was holding it in my hand, then I held it between my knees.

I was recently trying to do the cloud glitch on a emulator. I found this though. I had my reset binded to A + L. When I attempted the cloud glitch, I reset the game. My game reset with a save at Bowser's castle. I tried this again without attempting the cloud glitch and it had the normal save. I have tried recreating this on another emulator to no avail. I don't know if it is really a glitch or not.