Have you checked the server logs for error messages?

Are you checking the return code from system or open (I assume this is what you mean by '|')?

If you posted the relevant piece of code it would help.

This sounds like a "permissions problem". When you run the program from the command line, it has the permission of your log on id. When you run the program from IIS, is has the (severaly restricted) permissions of the IUSR_machinename account, which probably means that it doesn't have appropriate access to the directory or the file your are trying to encrypt.

This is a guess, but a quick check of the IIS server logs should easily tell whether it is a good one or not.