It's working again!
I have just installed Daily packages (1.3.1) on my RPi B+ and tested 1x1 and 2x2 exposure (both at 5% gain) and it's working ok.
So I think it's solved. I only note one thing, it bins 2x2 but does not increase signal, I should be forced to reduce either exposure or gain.
This is normal because of software binning isn't it ? That only happens in hardware binning right?