I haven't done one yet (I plan to shortly), and from what I've read in several posts, the orientation of the pump vanes and associated components is extremely critical with the operation of the unit. Your seals are fine.

Just a hunch...

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2009 ML350 (106K) - Family vehicle
2001 CLK430 Cabriolet (80K) - Wife's car
2005 BMW 645CI (138K) - My daily driver
2016 Mustang (32K) - Daughter's car