Hi Rotorman,
I am not familiar with the software you are trying to use to program your R-5 but I use a free application from Bob Parnass called TK5. The "normal" mode you referred to is just having the radio on. Clone mode is used to upload the contents of the radio to your program of choice or to clone to another R-5 (I think that is right).
You can download TK5 from Bob's site at
http://www.parnass.com
It is pretty easy to use and you can also copy and paste from spreadsheet files to it.
I have some sample files I can send to you if you would like,
I also am using the USB interface for programming my R-5.
Programming the R-5 can be a bear at first but once you get the hang of it you will find it easy.
Hope this information helps. Send me a PM or an e-mail to
kq4z@amsat.org if I can be of any more help.