Actually, this is not fixed.
I don't know if the problem is that I had installed and uninstalled JBridge a few years back. That has been a major pain ever since. It has caused every installation of a music software to have issues. Even after I have removed every remnant piece of JBridge, I have to click on an hundreds of error message for all the JBridge .dlls from prior initial install.
Once I do this then It will be fine from there on out. Every boot of S1 works fine.
Now, after I went through the same procedure with the installation of S1-4, I was still not seeing all my plugins. SoundToys was missing and then I just started looking through these Q&As to try and find the problem.
I'm now following the suggestion of danielkaminski1 in this post:
I've uninstalled S1-4 and am reinstalling now. It's in the process of scanning for plugins. Everyone is being blacklisted again. I'll have to patiently go through hundreds of JBridge error messages again and see if that works.
Meanwhile, I may not even produce anything in S1-4. I'll just stay with V3 till there's an update. It looks like many people having issues with the latest upgrade.