I know I am a bit late to this party, but the symptoms you are describing are exactly those which I get with a bent extractor rod.
The tolerance is that it must not be out of round (runout) exceeding .002 inches. I cannot perceive that small amount with my old, tired eyes without help, so I use the Power Custom Fixture to put the cylinder with attached extractor rod into the fixture, then spin the cylinder and observe the precision dial indicator to see if and where the runout is excessive, then bend it back into place. I can actually observe the excessive runout, but only if I place the extractor rod over a thin-lined piece of paper, line it up precisely, then spin the cylinder. Without the line for a reference point, I just cannot perceive runout of .002 inches.
My suggestion: reconfirm that the extractor rod is not bent.