My wife has a TS50, Blueprint, Manual, Brembos; OK I bought her the car - Wedding Anniversary!
Same Deal, Have only heard the noise once, at about 1500km's thought the'd left an Irish Mechanic in the housing with a drift hammer.
Circumstances - Car in neutral, clutch out; can't say I leave the car in neutral with the clutch out too frequently.
Now done 6,000km's, no dramas.
When I did the factory tour, they had a few boxes on show, pre and post the modifications. The modded box input spline was shimmed up so there was minimal backlash compared to th e original; don't know if this is related.
Otherwise, box is brilliant - wouldn't look at an auto for quids!