My Athena triple doesn't shift well at all on older cables. The cable drag must be critical. But that doesn't really explain your all-new system.

More info needed:
The difference in diameter of a 52 chainring to a 50 chainring is about 8mm. So the extra chain length wrapped around half the circle is only about 12mm, or about one extra chain link.
How much longer is your 52's chain?
Have you tried that on the 50 chainring?

Did you just swap chainrings, or use a different crankset?