I had one user, that set a lot of keyboard shortcuts, and every so often they would stop working. We found his user.mtx would not fully save, or became curruprted. essentially it was cropped, and the keyboard short cuts were not in the file. Once this happened, the file would not save again, and remained in this shortened currupt state.
I would take a look at your user.mtx, and make sure it is all there.
Like others suggested, have the user set up all their shortcuts, then save a role.
If the shortcuts "disappear", have them reload the role.
Note if they make other UI changes (add/re-arrange icons/tabs/etc.) they should save another role.
Production: NX10.0.3.5 MP16/TC11.2
I'd rather be e-steamed than e-diseaseled