You don't mention the discharge valves. They too can change the internal compresion ratio which changes the discharge temperature if they do not open correctly (to much spring tension or to small or area).
Since its the internal cylinder pressures that dictate ratios and temperature, there maybe a problem with the head on head end. Does it have pockets or clearance? some times the gas entering the cylinder can not fully distribute and the will be lower than suction line pressure in the cylinder which means the ratios on that end will be higher and so will the temperature at the discharge. Not only will it be hotter, but you throughput will be lower than projected.
A beta analyzer will tell you if you are having this type of problem. Cooper Energy Services presented a paper at the 2007 GPA conference where they discovered a problem with their latest cylinder designs and getting proper inflow performanace.