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I've had a few problems with BMW gearboxes myself.
A couple of years ago I had a (2nd hand but dealer purchased) R1100SS which would occasionally jump from top to fifth gear - a post on the Yahoo e-group at the time said that was quite commen, and it didn't actually bother me. Then the oil seal went causing the clutch to slip, and while that was being done under warranty I mentioned the gear box problem and BMW changed the box as well - total cost of about £2240 - virtues of a good warranty I guess!!
Last year I bought a brand new BCR - never jumped out of gear at all, but gearbox was excessively whiny (cue jokes) from day 1. That was changed under warranty when the noise persisted past the first service. I've since had to replace that bike following an unfortunate bike/tarmac interface in France but was fortunate enough to replace it with another BCR of the same vintage. I've found this one has the same whine, only worse, and also had the jumping out of gear scenario, again only worse. This will jump out of top into 5th gear before occasionally finding 4th (I think) and then a false neutral and bouncing the engine off the rev limiter. That is disconcerting!! It's booked in for a service next month and being checked out then.

davegooch wrote: ................but gearbox was excessively whiny ............. I've found this one has the same whine, only worse...............

I understand that hearing the noise from the gearbox is a function of the bellypan. They make the same amount of noise as the rest of the gearboxes on non BCRs (after all the gearboxes are the same) but the noise is reflected upwards by the bellypan. Thats the story anyway!!

Don't know about the jumping out of gear tho'.

Sandbar

sandbar wrote:
Don't know about the jumping out of gear tho'.

Sandbar

Ah!! After a while the old grey matter starts to stir and a couple of apparently unconnected facts start to re-arrange themselves!

At the end of 2002 - for the 2003 model year - BMW redesigned the gearbox on all R bikes. The supplier ( is it Getrag?) screwed up and a huge batch of bikes had to be recalled for new gearboxes. This was a deadly serious recall!! The dealers had to immediately physically go and collect any of the affected bikes, that had already been delivered. They were told not to ride them back but to transport them, and also under no circumstances were they to allow the customer to ride the bikes back to the dealership.

What was the problem with those gearboxes - there was a 25% chance that they would select 4th and 5th (or was it 5th and 6th?) at the same time.

That sounds awfully similar to the problem that you are experiencing.

Sandbar