Same problem here.
It seems that there is a bug in Start menu code, in the way that if you have more that 512 shortcuts in Start Menu.
You can check how many you have starting PowerShell with the command:
Get-StartApps | measure
This is affected not only by installed programas, but also by each shortcut in "All programs" created. So if a program installs a folder with shortcuts to 100 plugins, each one takes one slot.
Several solutions are provided that sometimes fixes things, others not. The only sure thing to do so far is going to
C:\ProgramData\Microsoft\Windows\Start Menu\Programs, and deleting any unnecesary shortcut, so the count goes below 512. After that, reboot may be not required, but recommended.
Many programs have one main executable shortcut, one uninstall shortcut, and several shortcuts that may be removed. My advice is to create a separate folder, and move there the unnecesary one instead of deleting them. As allways, procede with caution.
UPDATE: As 12th January 2016, it seems that with latest updates, Windows 10 Start Menu is working as intended, no matter how many shortcuts you have. If you still suffer this problem, ensure you have the latest updates installed.
UPDATE2: On 26th June 2016, Microsoft released a Windows 10 Start Menu Troubleshooter wizard that may help fix this: http://www.thewindowsclub.com/windows-10-start-menu-troubleshooter