Ok, I'm not very familiar with using that set-up as I use the serial port ALDL cable since I have a Toughbook CF-30 for tuning.
I did once try to use a USB type connection and had nothing but problems because windows was having issues with the com-ports, but that doesn't sound like your problem.
Did you make sure the port speed in TunerPro is set correctly?
Also check this post:
http://www.gearhead-efi.com/Fuel-Inj...ll=1#post13942
Bookmarks