Mal,
You have two potential water outlets for your pond (not counting the new outflow you installed).
The first is a leak through or around the old outflow that has suspiciously disappeared (or through some other spot in the dam). The second is the spring itself.
You mentioned using dye, I assume you have some sort of running or flowing water below your pond?
The easiest thing to try might be lowering your outlet, and lowering the level of your pond. Observe the outflow area when presumably most of the water is going through your outflow. Then raise your outflow back up above normal pool level. Observe the outflow area then and see if you can discern a difference. If so, then the dye could confirm your leak and maybe help you pinpoint where to dig for repairs.
However, you could be in the second situation, and your pond is losing water to the spring itself. You said that if you raise your new outlet even 3" the water level never gets that high. Does the water level stay at almost exactly the same level when you raise the outlet? If so, then it may be that the level of the spring sets the water level in your pond. Raising the dam and the new outlet will not work in that situation.
That is just one geologist's internet opinion - so it is not worth much without observing your actual situation.
My advice would be to keep experimenting with your pond. More data will certainly help in trying to figure out exactly what is going on.
Good luck!
