During an in-place upgrade from AX 2012 R3 CU9 to AX2012 R3 CU10 we experimented this problem :
After we had finished the Data upgrade check list (all steps were completed and marked as completed) we restarted the AX client and we discovered that we did not have any modules displayed on the screen.
After some researches on the Internet, it has nothing to do with checklists.
The problem was due to usage data.
Removing "NavPaneOptionsButtons" records solved the problem.
I just wanted to share this with you to avoid searching during hours
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