+1 on checking the wheel balancing.
Additionally, the mounting bobbins could also be the cause.
You might find the following info of use:
There are two types of front disk fitted to the 1200GS.
Newer R1200GS bikes have the bobbins pre-mounted to the disk, and the disks float. Integrated bobbins.
On older 1200GS bikes, the mounting bobbins are assembled when you fit the discs from the fitting kit, and its all held in place by the disk mounting bolts. I think there is less disk float with this system.
I think the changeover was for the 2008 model year (so end 2007).
Newer disks can be fitted to older bikes and vice versa, but the new system is better so I led to believe; less brake disc warping etc.
I only found this out when was trying to source discs for a 2nd set of wheels for my GSA in May. At the time, you could only get the newer style disc from BMW, and only the older style was available aftermarket (EBC, Wave etc). Of course you pay a price premium for BMW components...
So if you do end up changing your front brake discs, would recommend you go for the newer floating type with integrated bobbins.