Remote controller keypresses are buffered every 10-15 seconds

I have moved /home/osmc to the external usb stick…
After I have finished (fstab) all needed, I have restarted the RPI2.
During boot an update has started, so I ended up upgraded to the osmc September-2 version, so I cannot say whether the problem is related to the moving of the home folder or September-2 update.

From that time on, every 15-20 seconds I have delay with my tv remote connected over CEC that never happened before.

I turned kodi debug on, so I watched the log while I was pressing remote keys, waiting for a delay.
When I press the remote button and kodi ignores the command, in kodi log nothing is added, but then after a second or so, all remote keys are shown in the log and kodi acted accordingly.

Looks like osmc/kodi is buffering remote keys.
I don’t even know how to trace this type of error?
Where to start?