Assuming you're using the 'default' palette set (which is almost always the case), customizations that you make will be saved in a special location. So first, make sure the following line is present in your LabVIEW INI file:
menuSetup="default"
Assuming it is, after you've made the desired change to the pinned palette (moving NXG/Fuse to the top+expanded, collapsing Modern), make sure the following folder is present on your system:
[LabVIEW Data]\202x(32/64-bit)\Palettes\menus\default
Inside that folder should be a root.mnu file that has a mod date that matches when you exited LabVIEW after customizing the pinned palette. Note: while experimenting with this functionality, I discovered that sometimes the file is not saved. I couldn't figure out a difference between when I saw it get saved and when I didn't. But assuming you do see that mod date change, you *should* see that your menu customization is preserved between runs of LabVIEW. If at any point the INI file token is gone, and/or that folder in the LabVIEW Data folder is gone, that would reset your palette customization.
You can also use the Read Palette VI to inspect the contents of your custom root.mnu... the NXG/Fuse palette should be the first item in the items array after your customization.
P.S. - I filed Bug 2643687 to LV R&D to investigate why the changes sometimes don't persist between LabVIEW launches.
