It appears that I have a leak at the rub rail which enters the boat in the aft cabin.
Only a distant maybe here.
I had the same apparent problem about 10 years ago soooooooooooo, after several months of investigation I removed the interior foam/vinyl lining over the suspected leak. I didn't observe a leak in the suspected seam area. The leak was coming from somewhere up above and flowing down to the area of the deck/hull joint.
I installed a temporary cover over the area and observed for a year to experience all seasons. Rains like a bugger here in the winter. Never saw the leak from above the seam and never saw the seam leaking either. Permanently installed new foam/vinyl after a year and never saw the leak again and nothing after 10 years.
My advice, remove the foam/vinyl cover and be positive you've located the leak before doing "anything."
If it is an actual leak through the deck/hull seam and your rub rail is the same as my 1999 version :
It's fairly easy to get the section of rail where the suspected leak is located and heat it with a couple of (more than one) hair dryers and pull out the section of rub rail. About 24" on either side of the leak. Greater if it's a longer leak. The sealing operation consists of completely coating every surface, top and bottom, which could be subject to leakage with a sealant such as 3M4200. As extra insurance, layer the upper surface with an extra coating of 4200. Apply heat to the rub rail again and you and several friends press the rub rail back into position again. Once you are finished, apply a small bead of 4200 into the top joint between the deck surface and the rub rail as a bit more insurance to keep water out of the rub rail.
WARNING : you only get one chance at this. The 4200 sticks very nicely to the rub rail and inner portion of the rub rail and I don't mean that in a nice way as it will never let go. I experimented with every detail in doing this operation and it took time. Big thing is what temperature are you doing this and what is the working time for the 4200 ? How fast does the rail heat and soften when it is ready to be replaced ?
I was sealing a short section of rub rail leakage about 3 feet back from the bow :
I got lucky and managed to seal the leak and had it look perfect when the rub rail was pressed back into position. Use lots of masking tape to keep the mess under control.
Good luck with this as it's near impossible disassemble the flanges by cutting into the two flanges and inner liner as the whole mess is encapsulated in 3M5200 (otherwise known as the Devil's Glue)