When I had a leak spring up in a water pump that I had just resealed a couple of rides ago, I decided to investigate.
The impeller shaft has only one single row ball bearing on it. In order to hold a shaft on a single axis, you need a minimum of two. To address this, Yamaha inserts the impeller shaft into a machined pocket in the end of the balancer shaft so that that shaft supports the impeller shaft as well as driving it. The right side balancer shaft bearing then, becomes the second bearing on the impeller shaft, and the shaft is held on axis over its length as it rotates.
But here, I had a new shaft and seal already leaking. Something wasn't right. On inspection, I discovered that the right side balancer shaft bearing had a considerable excess of clearance. Measured with a dial indicator, it was over .015", clearly indicating a failed bearing. Because of the shaft lengths involved, .015" at the drive end of the impeller shaft would be exaggerated to around .020" or more at the seal, and since the balancer shaft is deliberately out of balance, it would necessarily force the drive end of the impeller shaft off axis as it spun, and the seal would have to try to follow that oscillation.
There is good news and bad news. The good news is that the balancer shaft bearings in the '06+ Gen2 engine can be replaced with the crankcases assembled and in the frame simply by removing both crankcase covers, removing the drive gears, counterweights, and bearing retainers, and driving the shaft out one side from the other. This needs to be done skillfully to avoid damage to the shaft, and it is important to note that the shaft has a flat side between the bearings that must be turned toward the crank in order for it to clear the crank counterweights.
The bad news is that the bearing is a proprietary sized double row bearing, and Yamaha wants $90 each for them. I've had no luck cross matching it yet, but I haven't given up yet, either. I did replace only the one that failed, though, and I didn't pay retail.
So, I suggest you check the balancer shaft bearing for clearance as you do any impeller shaft/seal service. You could end up avoiding a repeat failure, or possibly worse.
If the bearing(s) need replacement, check here for the details of the in-frame replacement process: