ok, I’ve been trying to set up custom menus for better work-flow yesterday and ran into the same problem. Any menu items not available at the start of zbrush (e.g. anything specific to a 3D polymesh or the symmetry options) was completely missing from my custom menus and the “shelves”. I am sure this is because the default active tool when Zbrush loads is the Simple Brush (which is 2.5D).
But then I realised that there may be a very simple solution, and it worked! 
the solution
all you need to do is reload your UI when you have a 3D tool active. and that’s all
. So after you created your nice UI and closed Zbrush:
- Open Zbrush
- Pick primitive, make polymesh3d / or load your custom tool
- Click on Preferences > Config > Restore Custom UI
Presto! all your UI elements are there were you left them
alternatively:
- save a separate UI file via Preferences > Config > Save UI
- Reload Zbrush
- Pick primitive, make polymesh3d / or load your custom tool
- load UI via Preferences > Config > Load UI
I’m hoping this will work for you if you had this problem