Rob, I've got an R1100GS with 49,890 Klm's on the clock as of now.
On June the 2'nd I pulled the shaft out to check the universal joints and lubricate the shaft splines, all three of them. I noted that there was no noticeable play on any of the universal joints and I then cleaned the male & female splines and then lubed them with spline grease (from local BMW club).
This weekend I've just done about 1,500 Klm's in the Snowy Mountains having fun in our winter playground. I 've just read your email and I went out to the bike and tested it. Here's what I found:-
No real noticeable noise, but............. there is the faintest clicking sound doing what you said you did. Backwards and forwards motion that is. I'm sure that there is no play in my universal joints so I'm thinking that there may be some slack in the male female splines. I know that mine are recently and correctly lubricated, maybe there is no lube in your splines and that is the noise that you are hearing.
However if you are hearing a noise then drop the wheel off, pull the brake caliper (& ABS if fitted) off and hold them around the footpeg frame, peel the rear of the rubber gaiter off and pull it forward, then remove the paralever bolt, then simply pull the reduction axle housing off (Diff to you and me).
Then you'll at least be able to see what condition that the rear universal joints are like, there are two of them that you can see at the rear end.
If you use 2 screwdrivers then you can easily pop the universal joint attached to the diff housing off for a good gander. If you also wish you can pull the shaft out and check the top universal joint as well. But pulling that one out requires a heat gun to loosen off the Loctite that BMW uses and a bloody great torque wrench to tighten the locknut up and an extremely small torque wrench to tighten up the allen headed bearing bolt retainer.
I would suggets that if not for peace of mind, then so that you can sleep, pull the diff off and have a gander.
It isn't that hard, after all if you have an 1150 GS then to check out the front universal joint at the gearbox end you have to remove the entire swingarm! That's obviously the price of progress, eh? I reckon the 1100GS is a better bike, don't you?
Mick.