There has to be a better way in the future. Looks like for now it's going to take a lot of time to find that special plug that keeps on giving. 

I also have this same problem and have just ignored it until now. I'm gonna see if the above suggestions will fix it. Thanks for posting Musicroom. And thanks for all the advice from everyone.

For me, my custom plugin layout still had lots of vsts left from my previous computer; many that I never bothered to install on my new machine. After deleting all the ones not installed, this layout comes up immediately like it used to. In X2 on this machine, it came up instantly anyway, so I never bothered to cull them from the layout. I guess good housekeeping is probably a good habit to get into for more than one reason.

Hey Jimbo, You got me to thinking about a quick test I could do after work. If this is layout related, then I will test the responsiveness of the fx bin with the default layouts. And/or try a layout with only sonar/cake plugins. (on that note, I do have perfectspace as one of my suspects right now) - I know, innocent until proven guilty.
 
 
 

Well I tried the other default layouts first and they came up instantly which led me to clean up my custom one. I'll keep my fingers crossed in the hopes it works for you as well.

I just got around to looking at this issue I was having with the delayed-context menu in X3.  I removed a greyed-out (uninstalled) plugin that was hanging around in my custom menu, and all seems to be well.
 
Thanks to this thread for that!

I'm having a similar issue when editing in the PRV, notes taking 3 secs to select or move. and if i nudge 5 times it takes up to 15 secs to complete. this is on a fresh project with only piano and tempo changes. x3d. :(

Removing the greyed out plugs definitively helped. Still there is something lingering inside of my setup that's slowing down X3. It now only takes 4 secs for the menu to pop up versus the 7 secs prior to cleaning up my layout.

Some answers sort of:
 
After cleaning out several unused plugs with an eye on older plugs, the right click popup menu from the fx bin was more responsive. The time for it to open went from about 7 secs to around 4 secs. I was also still experiencing choppy graphics when in console mode, so I had to keep working to solve. All of this behavior was happening on both new and older projects. So last evening I recreated a brand new plugin layout rather than edit a current one. I also removed all vst3 plugs that I don't use. Even Melodyne as a plug since I always use Melodyne in the ara track clip mode now. The results - everything is working well!! The right click fx bin menu pops up instantly and the console menu graphics are smooth now. I'm not satisfied in that I don't really know which of the many changes I made was the key difference maker. But at least I'm get back working and this in the "????" category for now.
 
Thanks for all the helpful chiming in here. Much appreciated.

It sounds like you did two MAIN things that could have had an effect.
1. Removed VST3 plugs
2. Removed old/unused plugs
 
If you want to nail down a bit more the exact cause (or help us figure it out too)...
Copy and save the new working layout under a new name.  Now you can mess around without worrying about screwing up what works.
 
I'd start with VST3 plugs because I don't see why they would cause performance issues with the context-menu.  So I 'assume' this would all go well :D
Start adding in VST3 plugs.  Do a few, see if it works ok.  Do more, etc etc.  If it starts loading horribly again, remove them one by one and see if any of them bring performance back up.

If all goes well with VST3, it was definately an old/unused plugin.  I assume by unused you mean 'uninstalled'.  I had one of those that was causing this issue for me.  ONE plugin was greyed out because I had uninstalled it but not removed in from my layout.  I removed that and it fixed my woes :)

If ur like me, you won't do this until you are super bored cause stuff works right now haha