I use an ftdi ttl logic usb serial converter to talk to COM2 (UEXT) on the mini and that works just fine, but when I tried the rs232 in/out or the TXD2 RXD2 nothing is sent, do I have to configure something to get this to work,.
I am not sure I understand your question. RS232 is COM1 and these are RS232 levels so you only need wires to connect to a PC, no level shifting.
Can you explain in more details what you have connected? How? Where? and a code snippet 
oh right so the rs232 out and in on the fez mini are already level shifted and this is COM1.
the UEXT has COM2 available (labelled RXD1,TXD1,RTS1,CTS1) and this can talk directly to an ftdi usb / serial ttl cable (these are really neat by the way).
and I presume that I could use COM3 using TXD2,RXD2 on the user 2x12 connector but I couldnt get this to work.
[quote]oh right so the rs232 out and in on the fez mini are already level shifted and this is COM1.
[/quote]
correct
[quote]the UEXT has COM2 available (labelled RXD1,TXD1,RTS1,CTS1) and this can talk directly to an ftdi usb / serial ttl cable (these are really neat by the way).
[/quote]
correct
[quote]and I presume that I could use COM3 using TXD2,RXD2 on the user 2x12 connector but I couldnt get this to work.
[/quote]
Where do you see TXD2/RXD2? Maybe schematics…yes this is COM3 TX RX pins on header.
You can also use COM4 as described here http://www.tinyclr.com/downloads/Mini/Broch_FEZ_Mini.pdf
So, you have 4 serial ports on this tiny module 
not counting the many other peripherals…
and of course in the near future you could turn the mini into a usb serial port and get a fifth virtual port,
I will check again for COM3 and COM4 thanks…