A year ago, we remodeled our main floor half bath. When we pulled the sheet vinyl off the concrete floor, we discovered a good deal of moisture (we were redoing the bath because of a musty smell). We cleaned the floor, laid a moisture barrier and wood flooring that matched the rest of the lower level, and reinstalled the toilet. The flange is now slightly below the floor level, but the wax seal seemed to squish nicely and the toilet seemed solid.
Now, a year later, there are dark water spots around the toilet. When I removed the toilet, there was definite water under it. My father had caulked the toilet to the floor so the water was not leaking down the back from the tank, but the water stain did follow the inside of the caulk line at the back of the toilet base. The water also came out the front and the right side of the toilet, following the seams in the wood floor. I never noticed pooled water, and there is no odor.
What is causing the leak? Should I add a flange extender? I cannot find any cracks in the old toilet. I'm stumped and I want to put a toilet back in soon!

My father had caulked the toilet to the floor so the water was not leaking down the back from the tank, but the water stain did follow the inside of the caulk line at the back of the toilet base.
Let's see. Take a wad of TP and rub it up and down the back and sides of the tank. Any moisture there? I don't think you'll fims any but I always check any way.
I would pull the toilet, clean off the old wax ring and reinstall using a wax seal with a funnel, (see image) and then caulk the base. Good luck, Tom

If flange is below level of floor, I would suggest using some spacers to raise flange. Or you could use two wax rings. One with the funnel, and one on top of that without the funnel. But, best bet is spacers, using two wax rings is iffy at best. Let us know what you decide.