The LP MB and the LP EQ (the original ones) are not found when opening an existing project.
Also missing are the Pro Channel modules PC3k Exp Gate, and VKFX Delay.
 
I can move the .dll files from my old folder, but why aren't they installed after running everything in Command Center?

The LP 64 MB plug-ins are not part of the current distribution. If you want them installed from the Command Center use rollback to get a prior version of the Engineering FX Suite. The two PC modules need to be installed from the files in your account instead of the Command Center.