I can’t offer a solution, but I can tell at least what is happening.
The OP describes the, what is currently known as, so called “Audio Forward Bug”. This is happening in WL7 and WL8. I can’t check if it’s the case in WL6 as well - don’t have it installed on my rig anymore.
What is happening, is that the audio stream is processed in realtime with the VST3 version, but while rendering, nothing happens. Slate Digital is just as puzzled as I am as user. The VST3 versions work fine in Cubendo and S1 in terms of rendering, but not in WL. Forcing WL into “run as admin” (as it is needed for IK Multimedia Plugins) didn’t solve this issue either.
Slate Digital and I had the impression, that it got something to do with the iLok routines. But the same issue popped up with plugins by Klanghelm - and that company doesn’t use copy protection schemes.
So yes… Unfortunately, Slate Digital aren’t the only people suffering from that strange bug, that nobody can explain so far. Eiosis and Klanghelm joined the ride. These companies are already in touch with the VST SDK team, but currently, there is no suitable solution.
Regarding the GUI recall issues - this is also already known to Slate Digital, and they are working on it. Actually a current software update should fix this, but unfortunately not the “Audio Forward Bug”.