Thanks for the response Noel. To answer your questions:
1) Yes, the same layouts are working in X2 currently.
2) Yes, I have all of the same plugins installed. I was using X2 last night with the same plugins without any issues.
3) Yes, I have the waves plugins in my layouts. It's not even that certain plugins are missing, whole subfolders are missing. For example, I have a folder called "Delay" for my delay plugins. Underneath that folder, I have two more folders called "Mono" and "Stereo" for different plugin versions. When I right click to add an FX, I only see the "Mono" folder. However, if I use the plugin browser I can see all folders. Here's a screenshot: ttp://tinypic.com/r/21dqv52/5
There are VST3 versions available for my plugins so that may be the issue but I didn't want to take the time just yet to update my layout for VST3 versions since I have so many plugins and I have to get this project done soon. Using the browser as a work around has been fine so I'll contact tech support when I get a chance. Thanks for the quick response!