Edit: first of all I should probably clarify I'm running an earlier version of Studio One, so please bear that in mind before proceeding.
I hope this isn't still a problem for the OP after nearly a year, but I had the same problem, and in case anyone else runs into it, here's what worked for me:
First of all, make sure you're cognizant of all your VST locations, as you'll need to find and re-instantiate them in Options>Locations>VST Plug-Ins once you're done.
Then:
1. Click 'Help'
2. Click 'Open Settings Folder'
3. Although this step shouldn't really be necessary, just to make yourself feel better copy the file 'Vstplugins.settings' to an alternative location.
4. Shut down Studio One.
5. Delete the file.
Now, when you next run Studio One the settings file will be recreated - with any luck, minus whatever machine-logical mental block it is that's persistently causing this issue in the first place. Remember that before you fire up any individual song, you'll want to go in Locations as described above and add all your VSTs back in one by one. If you're anything like me this won't be a problem as their identity will be seared into your brain by the experience of having to install them in the first place. Anyway, best of luck...
