I have a comparable story. My R12GS bought in june '05 was riddled with problems. EWS(stranded), FPC(stranded), rear ABS sensor, gear indicator sensor, fuel gauge, indicator buttons (L+R), corrosion(replacement), but when the servo brakes went bust I decided to sell after repair.
BMW dealership offered nice deal (trade-in) so I bought a new one in december 2007, thinking reliability must have improved. There've been some recalls (I could do without the extra trips to the dealer), but sad to say there've been some hickups as well (rear axle replaced when new, FPC stranded AGAIN, final drive seal leakage). Now at 54000km/36000miles.
But I honestly have no regrets in having bought this one.
I would never tell anyone BMW is reliable.
If it's reliability you want, go elsewhere.
Ducati stands on par with Suzuki as far as reliability goes (source :
http://www.ashonbikes.com/). Or go Japanese : Yamaha's future Super Tenere sounds promising, or else the Honda VFR1200 when it comes in enduro outfit. Both without chain.