You have to be sure that you are selecting the Pro-164. There are numerous scanners to choose from. When yo click the Upload to Scanner, be sure to choose the right scanner, and the correct com port, then be sure to hit the Start Download button. If your scanner is receiving data the bar graph on the radio will start to fill up and there will be a bar graph on your computer screen n which also will show progress. Do not pull the plug out of the radio until the upload is completed. You also need to be sure to use the stereo plug, not the mono adapter.
There is also a complete help file built into the program. Save all files so you can edit them in the future, naming them whatever you wish. And as was suggested above, be sure to manually step through the channel's to be sure that nothing is locked out.