During my 2nd free maintenance check up (25K-30K) the MINI tech said he had discovered a fluid leak in the input shaft seal of the transmission. (I have the 6 speed manual.)

He replaced the seal and now the transmission feels a bit different (for the better): The shift from 1st to 2nd does not go "kachunk" anymore and overall the shifting feels more "cushioned."

Has anyone else had this problem?

 

I bet the BMW MINI gearoil fluid for your 6-speed Getrag gearbox is new. That would explain the more cushioned feel.

 

New in terms of replaced with new fluid or new in terms of a new formula as well?

 

I would possibly say both. If you have the Limited Slip Differential, there is a TSB issued Feb, 2006 to use a specific fluid if you experienced grinding noises with the LSD taper rings.

...the transmission fluid should be replaced with Texaco MTF94 trans fluid (P/N 83 22 0 403 247)... This is a new formula that helps with the grinding noise experienced by some.

If no LSD, then maybe just the new fluid swap did the trick