I've emailed Unity about these problems and they've filed a bug on it...
I think there was a category mixup that's causing problems: the Visual Scripting category didn't exist when Playmaker 1.0 was first submitted, and now they're might be duplicate Playmaker entries. For example, when you make a new project, if you see 2 Playmaker packages, use the first one.
Are you able to import Playmaker into a new project from the asset store? If so, you could try importing Playmaker into a new project, then export the gizmos, itween, and playmaker folders in a unitypackage, then import that into your existing project.
Hopefully I'll get some answers back from Unity on how best to fix this problem!