Is your Jay Flight equipped with a Turbo Maxx, Fantastic or similar high-volume fan installed in your bathroom vent? These types of fans can move large volumes of air, similar to what an attic fan does in a home. If the fan's running in exhaust mode and your bathroom door is closed, it can restrict the airflow and create a slight vacuum in your bathroom. An RV toilet has no built-in trap like your home toilet, just a pipe that runs directly into your holding tank and, if the bathroom door is closed when you flush, it will allow air to be drawn down the black tank's vent stack, through the tank and up through the toilet carrying those gross odors you describe with it. To make matters worse, RV bathrooms are so small that it doesn't much to make it smell like you took a dump for three people.
The solution: Open the bathroom door before you flush or momentarily turn off or change the direction of the fan so that it draws in air (which will slightly pressurize the bathroom when the door's closed and push air down through the toilet when flushed, thus keeping the tank odors at bay).
Also, I agree with the previous poster that you shouldn't block the internal vent (if so equipped) on your plumbing. These do contain a one-way valve that only allows air to be drawn in, never out. If you ever detect odors coming from your internal vent, it's defective and should be replaced.
And as a final note, don't even bother looking at the gray/black tank level indicators. They're notoriously inaccurate after you use the tanks the first time. The only ones that seem reliable are the See-Level brand and they cost $$$ to buy and install. You usually only see these as standard equipment on high-end RV models. Get to "know" your tank capacities and monitor them yourself. I "know" my black tank will go for a week under normal conditions (just the DW and I) and I simply empty the gray on a daily basis. However, I "know" I can squeeze two days of use out of it if we practice water management when we're at a site with no sewer hookup. In time, you will learn this technique.
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TV: 2009 GMC Sierra 2500HD | Crew Cab | Std. Box | 4WD | Duramax/Allison
RV: 2000 Jayco Eagle 266 | FBS | TT -- 1986 Coleman Laramie pop-up -- Still in the family!!!