Yep. You'll never stop them unless you get the upgrade kit from Mini Mania.
Problem is that it is rumored the box is based on a Peugeot box, but Midland Gears (who supplied them) used substandard quality materials. The gearboxes never last unless you upgrade the necessary bits to the better quality parts.
There are 3 known failures (listed in most common to least common):
1. Second gear baulk ring wears out too quickly. Starts with cruncing into second gear and ends with it kicking it out of 2nd gear. Caused by weak synchros and the baulk ring teeth being too soft.
2. Diff slips. There is a ring gear around the crown wheel of the diff, so if it's slightly out of tollerance the ring gear will slip on the crown wheel and you'll lose drive. The Getrag boxes have the same design, but I've only been able to find one instance worldwide where a Getrag has done this.
3. The bearings let go. You were lucky in that they just made noises. Most push a shaft out the side of the gearbox. Since they are no longer making these anymore (now replaced by a Getrag 5sp) BMW requires a core changeover.
When mine spat a shaft (and dumped a big pile of oil in the apex of a corner - thanks to the local MFS for cleaning it up) I approached the dealership twice, and BMW Aus directly (there are no direct phone numbers so I put an enquiry through the send me a brochure link) they REFUSED to sell me a new gearbox because mine was too badly damaged to be used as a core changeover.
$10k later I now have a honking 6sp close ratio late model low km gearbox.
Thanks go to the Adelaide Mini community for getting me a few of the more important bits (gearbox, clutch) and to my dealer for letting me order parts they ordinarily wouldn't let you order (they prefer to only sell you the parts for your car, not parts for a totally different model)>