So, the portable x86 version is working correctly without any problems.
You tried to install the x86 version? To make your x86 portable version, a normal version, just close Sublime Text, and rename the Data folder, inside your portable folder, to something as Dataa, and open Sublime Text. After that, the issue persists? Even if you renamed/removed all the native folders as:
%APPDATA%\Roaming\Sublime Text 3
%APPDATA%\Local\Sublime Text 3\