I think you are right. I probably had some ports set up before flashing the ROM.
It would be interesting to see how am I oging to get out of this one

Probably even flashing the original ROM back wouldn't sort it as the COMs still wouldn't appear in the list.
Anyway, I came to the conclusion that it should work with the "enhanced network" as well as it does work fine on other computers and I tried to follow the links in boz's post
I got a tool (USB View) which shows that the USB is connected alright and the port is fine, but as soon as it is connected it is trying to set up a TCP IP connection which spends some time trying to aquire network address and then it fails. It would appear that the PC can't establish this connection to the phone. I am just going over the running services again to make sure that there wouldn't be anything else using this port.
Following this link:
ActiveSync 4.x Troubleshooting Guide - Connection Flow
I can see the route being added but I can't see any connections to that destination (netstat).
If anybody has any idea of how can I debug why this connection doesn't get setup, please let me know.
Cheers,
Dan