There's several items in this year-old thread.
@jjblough never responded back to let us know what happened after his 4 days on the water, and from his description of the problem along with the dealer's "solution", I'm going to guess that they fixed it with a clamshell fitting over the anchor locker.
I do not know if the OP visually observed water coming up into the ski locker, or if it was simply noticed the next morning. All solutions were assumed to be anchor locker drain fitting, and we have no way of knowing. I can tell you that I have observed this personally, same boat, and anyone with water in their ski locker can do a similar check - it'll look just like this:
That's my personal boat. The anchor locker MAY be the issue, but filling the ski locker while simply sitting at the dock overnight would NOT be the cause of that, initially. The anchor locker drain fitting usually manifests itself while in motion. Much like ALL of the issues of water getting into our boats, DO NOT ASSUME QUALITY ASSEMBLY BY YAMAHA!
The issue leading to the problem of water entering my ski locker was simple: NO sealant whatsoever on the bottom of the ski locker drain fitting. A hole was drilled to accommodate the drain plug, two holes were drilled to screw the fitting in, and that's all they did. The assembler also ran one screw in deep enough to damage the fitting - I have pics around here elsewhere to show this. So a combination of nothing sealing around the fitting and a damaged fitting before it was ever put in the water will allow water to simply bubble up, in, and around the fitting to fill up the ski locker while at rest overnight.
OTHER issues exist to allow water into the bilge in the first place, but this secondary issue is easily addressed with a screwdriver and some sealant, as long as a new ski locker drain fitting isn't deemed necessary.
I know this is a year+ old, but the way the design is, when there's finally enough water to trip the bilge, there is indeed a ton of water, I'd guess 15-30 gallons. When at rest, it'll level out, and if there's any weight in the bow, that'd get you the filling of the ski locker. It seems that it drains out of there around the fitting a lot slower than it comes in, but as long as the bilge is working, it only fills enough to make the ski locker wet, and freak you out when it's finally noticed, as the OP and myself experienced. Most I ever had in there was maybe 2", which seems like a lot, but opening up the plug and taking it for a ride emptied out all but the last bit that wouldn't wash over the fitting and down the hole. Takes forever for it to drain out too, and it'll never stay dry until the fitting is addressed, either with sealant or a new fitting + sealant, as well as the initial reason the boat has water coming in.
We don't use the ski locker anymore for anything that should stay reasonably dry, even after fixing it. It can get filled from below, and above, if the gutter and weatherstripping are insufficient.