EDIT: You've mentioned that 10kHz clockrate is used ? That's about 100ms integration time - at this times it is fucking sensitive
You mean 100us?
No way ! integration time of sensor is given as a time between two following falling edges of SH! Roughly 105ms at 10kHz it is !
Let's simplify it a little bit for explanation.
Each pixel behaves as a capacitor, which, when stroked with foton loses some fraction of its charge, otherwise it will stay intact.
At the beggining, when you set SH signal to high, all capacitors are charged to defined voltage level, then, after falling edge, voltage is disconected and pixels begins to integrate.
At the same time, rising edge of shutter caused that all charges stored in pixels from previous integration period are pushed into the analog pipeline.
There is a sampling amplifier on the end of pipeline. Each clock pulse causes one shift in analog pipeline trowards the amplifier. But the amplifier has sampling capacitance on its input - and this has to be discharged - this is reason why you need to generate RS pulse just before clock transition - to dischard voltage stored on its input.
After you have shifted all pixels, you might wait to integration time ellapse, or just start new integration period - so basically data what are you reading out is image registered on sensor during previous integration period.
Both RS and BT signals are used for some housekeeping inside sensor, so they must be provided continuously no matter what. (charge pumps for biasing and so on)
You have some pixels covered with lightproof material on beginning of array to help you with compensating for dark voltage of pixels (which is dependent on many factors, but temperature mostly).
But one particular thing is that when f2 is active, the output level gets a a bit higher, but still nowhere close to saturation.
Higher for saturation ? No, nooo. When saturated, you'll get lowest possible voltage on sensor output !
Also, confirm, that 2V/div scale on your oscilloscope is out of callibration, otherwise you're feeding in 3,3V logic.
Is it clear ?
Sorry for typos and mis-spelling if any, it's not my native language and I'm getting really tired now.