Ok, so I did as you wanted. First I encrypt the same 0 kb file in Visual Cron and then decrypt it. I didn't have the same issue.
Short explanation:
The problem is that the files are sent via FTP to us from another company. First of all VC download these files and moves them to the specified catalog, after that decrypted files and move to import. We often gets files which are empty. When the decrypted file is 0 Kb i get an output error: PGP File decryption error: Unexpected end of data