This is the way I run things on advice from my DAW builder.
Never, ever point your VST2 plugin paths (Devices/Plugin Information/VST2 Plugin Paths) to folders that result in you scanning both 32 & 64-bit versions of the same plugs.
The trouble starts when you need to use 32-bit plugins that are installed to the default location for shared plugins (C:/Program Files (x86)/Steinberg/VSTplugins) where that folder includes a mixture of both 32-bit plugins as well as 32-bit plugins that also have a 64-bit version installed too.
That last part is extremely important. Scanning both 64 & 32-bit versions of the same plugin will seriously wreck your day sooner or later.
Here's how we handle it (and we do not have plugin related troubles).
1 - VST3. With 64-bit VST3 there are no issues. You will usually let these install to the default location (C:/Program Files/Common Files/Steinberg/VST3).
2 - VST2.x. These are your problem.
With UAD, Steinberg & Waves I leave defaults.
With VST3 I leave defaults.
With VST2, I split into 3 folders:
A - C:/Program Files/64
B - C:/Program Files/32
C - C:/Program Files/32_Shared
Folder A is pointed to by 64-bit host
Folder B is pointed to by both 64 & 32-bit host
Folder C is only pointed by 32-bit host.
Usage:-
Install 64-bit VST2 to Folder A, install 32-bit ONLY plugs (those that do not have a 64-bit version at all) into Folder C. Install 32-bit plugs that also have a 64-bit version into Folder B.
Point your Plugin Paths to the right locations and close/relaunch - all should now be spot-on.