PGP is probably using direct access to the keyboard buffer, thereby bypassing STDIN.

The easiest way to verify this would be to create a file with nothing but a few (2-3) newlines in it and the pipe the file to the program on the command line. eg.

pgp --key-add temp_pgp_key.asc --with-private < nl.dat

If the program still pauses and waits for you to press return, it is bypassing STDIN (using getc() or similar) and your attempts to feed it a newline from within Perl are destined to fail.

Maybe one of the other monks knows a way around this.

If this is the case, it is quite possibly done deliberately so as to prevent your keyring being compromised by malicious software. If true, unless the program has an override for this feature, you may not be able to achieve your aim.