There seems to be a problem configuring the CWTYPE.ini file for the Active Com Port, PTT (RTS) and CW (DTR) line usage. Ok, fire up your favorite  text editor and display the CWTYPE.ini file.
First off, are you going to use the VOX?  I doubt it so page down to the section entitled [MOX] and set MoxOn=0 (MoxOn=1 for  VOX).
Ok now we need to set the Active Com Port and Com Port Type. Go to the section entitled [Osv_Cw] and look for the instruction KeyPortNumber. Set this to the com port you are going to use. Now look for KeyPortType and set it to 2.
So far, so good. Now the plot thickens! We are going to tell the software if you are going to use the RTS line or the DTR line for switching the Key input of the Radio. It is HEX digits that the program writes to the register. So:
         While in Rx and Key Off, program writes KeyOffTxOff
         While in Tx, and Key OFF, program writes KeyOffTxOn
         While in Tx, and Key ON, program writes KeyOnTxOn
         While in Rx, and Key ON, program writes KeyOnTxOff     This last one sounds a little strange but it does permit you to connect to some of the older rigs that use a negative voltage on the key circuit.

Remember this: 01 is DTR, 02 is RTS and 03 is both DTR and RTS
So lets try an example. I use Com Port 1. I prefer NOT to use the VOX but will build an OptoCoupler Circuit in my interface to key the rig via it's keying connector. Therefore I will be using the  DTR line for sending CW but do not need to switch the PTT in this mode so will not be using the RTS line. ( My interface now has an OptoCoupler circuit for each of the RTS and DTR lines.)
Uhmmm! so, what do we have? I set MoxOn=0, KeyPortType=2, KeyPortNumber=1, KeyOffTxOffByte=00, KeyOnTxOffByte=00, KeyOffTxOnByte=00 and KeyOnTxOnByte=01.
Lets try it eh!
         While in Rx and Key Off, program writes KeyOffTxOff= 00 hence I get no RTS or DTR activity. Transmitter is not sending and no CW o/p.
         While in Tx, and Key OFF, program writes KeyOffTxOn= 00.  Ok! since the combination Key Off and Tx On is not an option in CW we disable this instruction with a '00'.
         While in Tx, and Key ON, program writes KeyOnTxOn=01.  This is the Keydown combination so now we have DTR line active and the CW is being transmitted!

The Semi and Full breakin switch on the rig works as normal. 

         I hope this helps a bit. It does sound a tad complicated eh!