The tank/reservoir should be large enough to keep the suction inlet under fluid, and the tank still be large enough to hold all the fluid when all cyl's are fully collapsed.
From what you say, the cyl appear to be connected in series, whereby the second cyl only moves when the first cyl is full. In retract mode, the second cyl will empty first, and then the first.
Does the first cyl make the valve go into relief, and even if it did, the relief pressure would be at the input to the second cyl.
You just might be running out of fluid for the cyl, due to low tank volume.
Have you used a hyd pressure gage in the lines to see if and where you have pressure?
If the pump is running, and there is fluid at the suction side of the pump, the available fluid is going somewhere.