Thanks for the responses everyone! I've tried whats been suggested but to no avail.

I think this is a bug as I've seen another thread that makes reference to the same issue.

I'll put in a tech query when I get round to it.

YES, this is what I am experiencing now!
 

jpjones14
I have seen this same issue. I believe it to be a glitch. Sometimes the layouts seem to work in the browser and sometimes they don't work when trying to add a plugin via the FX bin.

I had the same issue as well.  I have been out of it for a couple years.  But, just upgraded my machine and started fresh, now i am remembering the old problems I had forgotten. One was a panning problem which I seem to have figured out, this was another.
I can only assume this bug hasn't been addressed. I just installed the latest X3 and the problem still persists.
While I don't have a fix there is an easy work around.

When you R click on an FX bin, instead of managing the layout through "Audio FX", go down to "Soft Synth" and edit the layout through there.  You can create a layout through the "Soft Synth" option, then name and save it.
Then R click on FX bin again, this time go to Audio FX/ Plugin Layouts and select the the layout.
Worked for me!
For whatever reason it wont save the layout when you edit it through "Audio FX", only if you edit through "soft synth".
 

I have found a workaround for this x2a bug - instead of starting with the "all plugins" list and modifying it to how you want it, start with a new blank list and add all the plugins you want from scratch.