I wish I could give some insight on that but anything I might know, you probably already have covered.

Did you handle the rebuild of the mast cylinder yourself?
I ask because if you did, you would/should know the condition of the cylinder bores and pistons.
If you farmed that out, did the rebuilder indicate any damage or defective conditions to any parts?
The only other things I can think of would involve shavings shed from pump parts migrating throughout the entire system. If that were the case, I would think there would be other cylinders showing some issues too (unless they have issues already in the works).
For the problems (shavings in tank and leaking lift cylinder) to have been in the lift cylinder before the rebuild, and the same problems persisting with the same cylinder affected............that is almost too much for me to think "coincidence".