Andrew, this is just a shot in the dark so take it as a fwiw.
I remember reading about an issue that could develop at the trans tail seal if the T/Q on the beam bolts is over the specified value, and ( this is where my memory fails me ) if the C-beam is not centered correctly. Apparently bad alignment and or T/Q on the beam bolts distorts the tail housing causing a leak.
Okay, here goes my screw ball reasoning!
If that can happen at the trans end of the beam, why can't it happen at the pinion end of the beam.
I do believe I read this in the Q & A section over at Bill's site, zfdoc.com.
http://zfdoc.com/
I wish I had better command of this subject to give you some better thoughts to help solve this issue.
Tom