Hi!
I'm using NOD32 myself and I cannot confirm this problem. I just did a scan of the BoxCryptor folder and NOD32 does not report any problem. See a screenshot of the log file here:
http://www.troovi.com/xGCwMZ5nJKsR
I can assure you that BoxCryptor does not contain any malware!
--Robert
PS: Some kinds of malware inject themselves into other files. This could be a reason for your problem.