Are you sure that breather is coming off the PCV's at the top of the rockerbox covers? It would be attached to PN 16 in the diagram posted earlier. If it is, then that is the breather reroute that is most common with our bikes. If that breather is coming from somewhere behind the rear cylinder, in between the starter and the rear cylinder, then it's your transmission vent line. If that is the vent line, then check your fluid levels. I believe an over filled primary might cause the transmission vent line to puke oil.
There's also a seal that causes the vent line to puke oil.
BUT if that is NOT the transmission vent line then you have no worries