from the way your question is stated...i think your calling the sockets on the mother board, where you plug devices into, com ports. their not. YOu can put a modem in the first slot and it may use com 5.
one has nothing to do with the other.
com ports, in the sense your talking, are logical devices.
why can't you use com 3?
almost all software, even fairly old software can use up to com 4 with no problem. With very new software any port will do.

whats not working?