On early models the controller was a problem, but I don't know about later models. Fortunately it was easy to replace. On my 2004 GS the controller was replaced even though it was still working. I don't know if I've still got the original controller lying around somewhere, as I kept it as a spare in case the new one failed.I think the problem was that water could sit in the depression in the tank cover that had the controller mounted on it. Maybe you could dry it out and see if that helps?

That's the one. The cover is easily removable.If drying it out doesn't help there is actually a 'fix' used by a number of owners. A directly wired bypass or a bypass cable. Do a search for r1200gs fuel pump controller bypass and you'll get pointers to descriptions on how to do it yourself, or to someone selling cables with connectors. Including this DIY one from advrider:http://www.advrider.com/forums/showthread.php?p=2768376Good luck.