Perhaps the problem is the planetary gear inside the starter engine. If the outer ring gear is loose, the starter engine may turn, but it only drives the loose ring gear and not the axle of the starter gear that in the end should drive the crankshaft. There is an official Yamaha spare part to solve this problem and I bought it, but I didn't use it, because I couldn't imagine how it should work properly (it is just a disk that, when mounted, probably should increase the pressure onto the ring gear to keep it in position). I finally solved the problem by drilling a blind hole through the case of the starter engine into the ring gear and by putting a pin into the hole which fixes the ring gear to the starter engine case. Of course you have to stop drilling before you reach the inner side of the ring gear with the teeth.
This happened 12 years ago and still works fine (though I don't drive that much kilometers per year). I'm not sure, but probably I found this tip here on tr1.de somewhere in the old forum. By the way, there is a useful explanation of panetary gears on wikipedia (entry "Epicyclic gearing"), which may help to understand the problem.