@Big_D
Check first to see if they failed to scan.. that would be indicated in Preferences->Plug-ins->VST->Re-scan (button)->Plugins that failed to scan.
If listed there, then you have some troubleshooting to figure out. If NOT listed there, then it's just simply because you haven't included the location where the .VST3 files for these manufacturers are located.
I know waves puts everything in a shell (WavesHell.. oops, I mean, WaveShell.dll). But they install those in C:\Program Files\Common Files\VST3 by default, so make sure that you've included that in your VST plug-in paths box in Preferences->Plug-ins->VST
Waves also has different shells for different versions of plugins. Some of my plugins are version 12, some version 13. Double check the versions of the plugins you don't see vs. the ones you do see. If they're different, that may be a hint that you need to either locate the shell for the one version, or you don't have that version installed.
Here's a sample of what I mean of the different Waves shell versions I have:
https://i.imgur.com/kSEtxeM.png
I dont have any Plugin Alliance stuff though, so can't speak for those.