Let's apply some logic
If the holding tank is empty (or close to it), and the inlet from the toilet is at the top of the tank, how can it be tank contents that are running back toward the bowl? They can't jump up into the hose. However, if it only happened while you're sailing, it is possible for heeling to send the contents of even a half-full tank back down the intake if the inlet fitting is next to the hull instead of toward the centerline. But if it happened while the boat is at rest, there's no way it can be tank contents.If it did happen while the boat's at rest, either the tank isn't empty, but IS full to overflowing (Did you check to see, or just assume it was because you pumped it out?), or what you're seeing isn't coming from the tank, but is runback of waste in the head discharge hose. There are several possible reasons why the tank may not be empty: 1. the vent is blocked (usually a clog in the thru-hull), preventing it from being pumped out; 2. you left a seacock open that allowed it to flood. So first, make sure the tank IS empty.If it is, then it has to be just what's left in the hose between the toilet and the tank. It's dirty because the inside of the hose is dirty. If the hose runs uphill all the way to the tank, gravity will send whatever is left in the hose back toward the toilet. Turning the y-valve and opening the seacock allowed it to drain overboard.Two possible reasons why it's a new phenomenon: 1. the "lips" in the joker valve in the head discharge have finally stretched open to the point where they're allowing the toilet to flood. Even a new joker valve can't prevent very slow seepage, but with use the "lips" become more and more open till it's no longer a one-way valve any more. 2. Sea water calcium carbonate buildup in the head discharge hose to the point where it's reduced the diameter of the hose enough to restrict flow and create backpressure. 3. A combination of 1 and 2. However, if this is your first season with a brand new boat, it's awfully soon for either one to be happening unless you're living aboard and spending 24 hours a day aboard. Otoh, the weather has been very hot on the Bay this summer, which means the water is warm...and calcium carbonate buildup happens a lot faster in warm sea water. So you have several things to do: check the level in the tank, check the tank vent thru-hull...remove the discharge hose from the toilet to see what the inside of the hose looks like and while you have it off, replace the joker valve. If none of the above solve the problem get back to me.