Having many programs with Shell Overlay Icons in Windows will cause some of them to not appear. This is because there is a limit to how many Shell Overlay Icons. (Not sure but I think it’s around 10 icons)
Below is an example of a Shell Overlay Icon.
To overcome this problem you need to run “regedit” and edit the registry entries in the path below:
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\ShellIconOverlayIdentifiers
Just delete any entries you don’t need and restart.