So far it only reproduced with Voxformer and Spacifier, so maybe it is limited to those plugins. Voxengo has confirmed that they can reproduce it with Voxformer so it isn't limited to my system.

Just to be clear... The button that should be used to disable/enable the plugin is the small one next to the plugin as it is shown inside the track's FX bin, not the bypass button in the plugin window itself. The one in the plugin window itself doesn't exhibit the problem.

Not sure if related, but I opened up a couple old projects which already had FX bypassed and had to click them twice to enable them. This has only occurred after first opening a project though, and after initially enabled (with two clicks), they then go on/off as expected. I am not sure if this is related to the OP, but I have noticed this on non-Voxengo plugs.

It sounds like it could be related in some way. Thanks for the info, every datapoint helps.

I've noticed this behavior with the gliss eq.