Just today I replaced the Jabsco manual pump-to-bowl hose- 15inches long.
If any part of your toilet is at or below the waterline, there needs to be a vented loop in the intake and if you check the installation instructions for your toilet, you'll find a drawing which shows that the loop belongs between the pump and the bowl. So unless you replaced that 15" hose with two hoses at least 2' long with a vented loop, you need to do that, 'cuz relying on the wet/dry cam--especially in a Jabsco toilet--to keep the water outside your boat from seeking its own level INSIDE your boat when the intake thru-hull is open is a good way to sink your boat...or just have a lot of water to mop up if you're lucky.
I winterized in December by flushing alot of freash water- and antifreeze- through the entire head plumbing system. (That's what I do after every sail.) The clear hose was COATED with black whatever grows in the bay water, so I assume the pump is also.
A) Clear water hose is not rated for below waterline connection. It also allows light to penetrate, algae--which is at least one of the things growing in your hoses, needs light--which clear hose provides. However, black flecks are also likely to be the dead and decaying remains of animal or vegetable sea life that's gotten sucked into the system. Your toilet intake hose should be sanitation hose...Shields or Trident #148 will be fine.
SO even after I winterized well, there was still the black stuff flushing into the rim and bowl. In short, you need to flush that rim. After all, it will be just a short distance to your butt.
Remove the inlet hose and connect a 2-3' length of hose to the pump that you can stick into a bucket of water to which you've added at least a quart of distilled white vinegar. (Or, if your head intake line is teed into the sink drain, replace the intake line with a new clean hose and fill the sink instead of a bucket). Flush the whole bucket/sinkful through the system. Repeat...until no more black flecks are are coming out of the rim of the bowl. And then install a filter in the intake line...in a location above the waterline that's fairly close to the thru-hull, but still accessible to clean out regularly.
You should have done this BEFORE you winterized.