How to allow a program

How do I configure comodo 3 to allow a program total access to internet without restrictions? I’ve tried giving flashFXP free access, specific ports and all other settings I can think of, but I’m unable to connect to my brothers ftp-server without going into passive mode. This goes for other programs as well.
Such as with DC++, I am unable to get any search results without enabling passive mode.

Why is this so?

There are some notes on this issue on the FlashFXP site