Hiya,
I have a very similar boat to yours. A 1969 14' Traveller with the same subfloor compartment/bilge setup. It too would take on water into the sub floor. It didn't become problem until I started leaving it in the water between weekends. When I pulled the side drain plugs, there was lots of water in there after sitting for days (basically the compartment was full). You couldn't tell that the boat had taken on water until the side plugs were pulled (unless you notice the added weight).
On mine, it was failed sealant on a transducer that is mounted on the bottom surface of the boat. A tube of 3M 5200 cured it.
Now here's my issue... Although I have a similar boat, I don't think it's a very good design. It is using the under floor space as a sealed chamber for "floatation". That means that any water that gets in there is trapped by those side plugs and stays in there to cause rot. I have removed the side plugs (realizing that I have thereby eliminated the floatation designed into the boat) and let the under floor space drain into the bilge. At least I can tell when the boat is dry. I haven't replaced the floor on my boat (it's fine), but if I were to, I'd probably make a centre void/channel, and then add foam in the other parts of the subfloor. To be honest though, my boat is a bit of a "beater" with the original chrysler on the back. It keeps working for the few hours per year I use it on a small lake, but I doubt I'll revive / restore it if I still have it when it dies. I'd rather restore a bigger aluminum boat.
Is the void to the subfloor also sealed at the front, under the deck? If not, maybe a leak up front is dribbling into the void. I'd just take a sharpie (pen) and a bright light and go over every inch of the hull on the outside looking for either a hairline crack, or a small pinhole defect in the fiberglass. Mark anything that looks suspicious. Too bad you didn't go after it when you redid the floor/stringers. You could've cut some big access holes in the old floor and then floated it to find the leak before removing the stringers etc..
If the compartment is sealed in the front too, here is a hair-brained idea... Maybe you could rig up a bicycle pump to one of the side drain plug holes... If you floated it and had someone pump some air (to pressurize the compartment a bit), maybe you could see bubbles coming from the hull on the outside... Of course you'd have to float it in deep enough water so you could play "frog man".
Take a crayon to mark the hull if you find a leak. I have no idea if that would work, but it's the type of thing I seem to end up trying. Wifey reminds me of my goofy ideas when she always ends up helping me (e.g. working the pump in this case). But, sometimes they work.
Good luck.
