I got PuTTY sorted out. It was a matter of newline and linefeeds. The built in serial monitor (and my Arduino code) was looking for newline to end a command, but putty was using linefeeds.
I've made the Arduino code smarter in that regards and I am able to use PuTTY with no issues.
Anway, the PuTTY was a sidetrack I went down. My real concern and issue is with Perl.