I've got a similar problem with a different bike. I have a 1004 Wee Strom(DL650). On a ride when I first got it I had a clutch problem and had some bad down shifts. The clutch wasn't disengaging all the way because of a bind on the lever.
Since then It up shifts easy but is clunky on the 3rd to 1st down shifts. If I double clutch and rev the engine I can mesh them OK or if I do it at really low speeds. But on the fly it's clunky.
Probably dinged the synchros in the one direction.
Replacing the clutch won't make it go away, a new set of synchros will probably make it better but unless it really goes to hell, I'm not splitting the cases.
For the engineering bunch, it may be the shift dogs but that's too technical.

 

Can't really help you Steve (except for the advice to get a second opinion from an other BMW motorcycle dealer if the first one is unable to help you) but I moved this thread to the forum section where it belongs, the GS (& F650GS Twin) section.

 

Thanks for moving my thread Karim. Yes have tried a few dealers, but being out of warranty now (even though the problem was reported under warranty) has made these guys less than enthusiastic. Splitting the cases for my own account especially if I am not sure they will find any obvious damage that they might or might not accept under the original warranty is quite risky. Stumped for now!!

 

I know you might have thought of this but check the gear lever linkage. It could be nothing more than sloppyness at the lever.

I had the bolt come loose on a splined shifter on a Suzuki many years ago and exactly the same problem. The lever would reach the end of it's travel before the gear was fully engaged.

 

Hi Trevor checked the lever is tight. Either I have to consciously downshift the lower gears at slow speed, OR open the gearbox. Tough one! If only I new exactly what gearbox part controls the shift action. Would be easier to understand what has to be done.

 

Everything else about this bike is brilliant. Esp with the Wilburs springs and touring seat.