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Not sure but it appears that you had the "rotating type" valves in that motor. These were the 1951-53 type and would have had the shorter spring along with the 2 piece valve retainers as shown in your picture. I am attaching a pic link for comparison purposes.
The rotating type valve had a slightly different stem....the keeper groove is in a different location by about .005". Plus, as I stated, the spring is a shorter length. The 39-50 springs were about 2.40/2.48" long and would NOT be used with the rotating type valves. The 51-53 springs were 2.20" long and would ONLY be used with the rotating type valves.
I'm guessing that in the rebuild, the wrong springs were used with the setup you have. I would also check the valves to see which ones you have. Measure from the flat face of the valve head to the first edge of the keeper groove. The 8BA valve (49-50) was 4.49" to the groove. The 1BA valve was 4.54". Just make sure all your valve parts are matched correctly before you put it back together.