Did anyone inspect the vent pipes to make sure they were installed correctly? Try also posting this on the Plumbing forum. I found this on another web discussion site: "It may be that you have a leak in the sewer stack, and that the expansion with the hot weather is whats causing it. Cold weather contracts various things and may seal it up again. I too am the type that I can smell things in parts per billion (reason why a lot of times, the Superintendent would ask me how the plant was doing, because I was the first to be able to detect things at the Waste Water Plant). Another possibility is that something is in your attic and its coming down through cracks in the ceiling or through the walls, in your bathroom, (dead squirrels or some critter). Now, make sure, to check your TRAPS in the shower or bath. its possible, that you have a plugged up soil stack, (though the plumber should have found this, if he checked the roof), and that when the temperature gets warm, or something happens outside, it sucks down the water from the traps in your bathrooms, (like when you use your sink in the kitchen and it creates a vacuum and draws down the water from the traps if the pipes aren't big enough...)"

Water can travel in the most unexpected paths as it makes it's way from its source to where it finally indicates itself. If you think it might be the recent rains and the reroof, If you have access, I'd recommend someone check the attic. Look at any penetrations through the roof. See if you can note any wetness, or discoloration that looks like recent wetness. Water can enter the roof assembly in one area and travel along the roof framing quite for a few feet. If there is insulation on the attic floor, you may find moisture when you pull the insulation back. Whoever goes up there, have them bring a cellphone up there and take pictures. With the recent reroof, there may be issues with the bathroom vent boot and how it was flashed. When reroofing, it makes sens to replace flashing items like a vent boot. They're only a few dollars. If it's a sunny day, see if you detect daylight coming in from around the boot. If water is indeed getting in from around the boot, depending on how your drain/waste/vent plumbing is arranged, water could be flowing down the vent pipe and entering the bathroom through the wall at the back of the vanity, and that's why the vanity was wet. Could be any other roof penetration as well. An exhaust vent. Chimney flashing. Someone can walk the roof and look for exposed fastener heads. Good news is the panels in your drop ceiling can easily be popped out. See if you can trace the path the water took. Those separate puddles may be coming from a singular source. Your comment "Our toilet bowl does have water running into it....", if the toilet fill mechanism is running, excess water in the fill tank should flow into the bowl when the water in the tank level reaches the top of the overflow tube. The overflow tube will flow the water into the bowl. When the water level in the bowl becomes gets to trap height, it will automatically flow out through the trap. Toilets. I've seen the water fill tube in the tank become disconnected and spray water out between the tank and the tank lid. If that was the issue, water should not have gotten inside the vanity. Same for a basic toilet leak; cracked porcelain, a failed wax seal, etc. And since the water indicated under the vanity, check the underside of the sink and faucet. Turn the water on. Make sure the stopper assembly, where it enters the sink tailpiece, is water tight. Close the stopper to fill the sink. Open the stopper and let it drain. Look for cracks in the porcelain, check the putty around the drain, look for a loose or disconnected waste pipe. About two months ago I came across an under-sink PVC trap that was snapped cleanly at a union from storage items being pushed up against it. The waste plumbing looked perfect, it was only by putting my hands on the trap assembly and moving the pipe that caused the plastic pieces to separate, showing the cracked pipe. Good luck with this, I hope it's something obvious.

There's little doubt that it is running down to that point from somewhere else. Leaks in flat roofs are notoriously difficult to pinpoint. Frequently it's from a place where the flashing has failed, either from a vent pipe or a transition area from another area, wall or roof. Backed-up gutters and downspouts are another possibility. Pictures from above the roof might aid in giving more specific suggestions.

Water flows downhill. It could be your upper windows are not adequately flashed. It's always useful to see what's happening when it is raining. Go out in the next windy downpour and look. We had mystery water leaking and crawling around under the porch in a downpour --- utterly miserable --- made everything blazingly clear. We fixed the problem and have had no more water in the basement. The fact that the door has an awning suggests flashing is an issue.