I have been using Mod Organizer 2 for my Skyrim Legendary Edition mods for a while now and it works great. Yesterday, I finally bought Skyrim Special Edition because I wanted to try TechAngel85's SSE Guide and it seems like most of the work on this site is focusing on Special Edition.
I followed the installation instructions in TechAngel85's SSE Guide. Downloaded the latest Mod Organizer 2 file from Nexus. Have tried with both the Standalone version and the installer version. The installation goes fine. I install in my ...steamapps\common\Skyrim Special Edition\Mod Organizer 2. (My other copy is in ...steamapps\common\Skyrim\Mod Organizer 2.)
But when I ask it to launch Mod Organizer 2 at the end of the installation it launches my Skyrim instance instead of Skyrim Special Edition. TechAngel85's guide says it should open a dialogue to ask if I want to install another instance or portable, but that dialogue doesn't open for me. Also if I navigate to the Special Edition folder and click the Mod Organizer 2 exe file, it opens the Skyrim version.
What am I doing wrong? Or is it not possible to install instances for different games? I have searched for the answer to this, but cannot find it. I'm sure it is something simple, but I have tried various things without success. If anyone has successfully done this or knows that it isn't possible, help is much appreciated.