Difficult one eh?
It could indeed still be the keyfob.
As far as I'm aware, the indicators should always flash when using the remote. It's telling you the fob put out a signal and the skreem received it.

I still think it could be a fob issue, but don't really know where to go from here now. The skreem is a sod to get to, so you don't want to be replacing it until the fob issue is 100% ruled out I suppose.