I'm running win 8.0 I will try to use a win 7 system. I had problems with the makerbot desktop program also. It might be the in the settings on laptop I'm using.
I was trying to do the update to sailfish and going from the install doc on the Jetty page it mentioned downloading the MB desktop program to get the dual extruder offset setting.
The main trouble I am running into is that my CTC was build last year after all the software and updates listed in the instructions are ether out of date or cant be downloaded.