Per the Owner's Manual, the 899 would start in gear if the side stand is up AND the clutch is pulled. Should the stand switch be broken (bike thinks the stand is always down), the ECU will cut the engine as soon as you put it into gear. Since you didn't mention this, then I would guess that the problem is the clutch switch. First of all, take a look and make sure you hear it clicking when you pull the clutch... if memory serves me well, the switch has a little blade that gets pushed by a pin, check if the blade is bent or the pin is bent, or anything mechanical. Next step is to find a place (a connector) where you can put a multimeter on the terminals and see if it really works.