Hey guys, ran into the same exact problem and these are my steps to how I fixed the problem for Windows 7.
Downloaded:
-"Axe-Fx II Firmware Version 11.0"
-"Axe-Fx II USB Setup ( 168 )" for Windows (updated Aug 13, 2013)
-"Axe-Edit 3.00" for Windows
Next I downloaded a
"system reset file", in the link; below there is a "Clean system data file for firmware 11" SYX file, which I also downloaded.
Warning, before uploading this file into your Axe-Fx 2, you should save EVERYTHING, this is also the most crucial part of fixing the problem (at least for me).
Now because you can't send these files to the Axe-Fx 2 via Axe-Edit because you can't connect to it...
I downloaded the Fractal-Bot to upload the files.
FIRST, backup all your presets, cab IRS, and any other settings before uploading the system reset file.
1) Install "Axe-Fx II USB Setup ( 168 ) for Windows" (updated Aug 13, 2013)
2) Upload "Clean system data file for firmware 11" SYX file via Fractal-Bot
3) Upload "Axe-Fx II Firmware Version 11.0" file via Fractal-Bot
4) Install "Axe-Edit 3.00"
Now you should be finished! After installing Axe-Edit 3.0, you should be able to run it and it should connect to your Axe-Fx 2!
Hopefully that helps...