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When I went to play some custom levels, all my levels were gone!
When I click the custom folder, it says "C:\Program Files (86x)\Marble Blast Platinum 1.14\marble\data\missions\custom is not accessible. The file or directory is corrupted and unreadable.
... You might want to run CHKDSK. At the very least. If it says the folder is corrupted, then the filesystem is corrupted. This could also be why the game wasn't opening Beta 3, if the game could not read files.
Note that since it may affect that folder and the game as well, it's possible that other parts of your disk are affected as well. This could mean the disk has issues, and a backup would be advised.
Less likely could be malware, but you should look into it.