I tried deleting both “%APPDATA%\Sublime Text 3” and “%LOCALAPPDATA%\Sublime Text 3”.
Portable version behaves the same way. Running with admin privileges makes it work, but it looks like it doesn’t fully interact with the OS, as I’m not able to drag and drop files to open them, nor access my network drives.
Running Portable without admin privileges ends up on a new crash/freeze after moving the mouse over its screen.

Now I remembered, I am also using the x86 version, just because of this kind stuff. For may experience, they are more trouble makers than the x86 version, as on Windows, as on Linux. Also, I do not see why Sublime Text needs a X64 version. Does it is planning to use more than 4 GB RAM? May be it is for performance as the x86 support on x64 machines being by virtualization: