Microsoft engineers seem to have placed some sort of limit on the total number of menu Apps to 512 entries. If you have over this amount they will not show up in all apps. And only apps in the start all apps menu can be pined.
To find out how many you have follow this instruction:
1- Right click Start
2- Left click RUN
3- Type POWERSHELL
4- Click OK
5- At the promp type Get-StartApps | measure
6- Press ENTER
If you see a number larger than or equal to 512 you are affected by this issue.