The stop rod dosn't have anything to do with lowering, it simply kicks the control lever back to neutral. On older tractors, if it was misadjusted the 3PH could lift too far and damage the seals on the piston, but you have already proven the seals on your piston are OK. I don't think this is an issue on later models as they(Jinma) fit an internal stop block to the inside of the rear cover plate that physically prevents the piston from extending too far out of the cylinder when lifting. My 2005 model has this stop inside the reservoir.
The relief valve assembly is ON/a part of the 3PH control valve located under the right side of the seat. the control lever connects to the valve. If the shop that serviced it checked the relief pressure of that safety valve, a piece of debris may have found it's way into the valve at that time.
I should have suggested that you flush the valve yesterday which may fix the issue right there. This is easy to do without disassembly of the valve. Screw the speed regulating valve knob all the way in till it is tight, then start the engine and try and raise the 3PH. The hitch should not go up as you are blocking flow to the cylinder. This forces the relief valve on the control valve to open and forces fluid thru it. This may clear any debris in the relief and restore normal function...