Yes, worry.....until you find out what it is. It may be something that can be safely ignored or may be a problem that needs attention. Never ignore suspicions of leaking until you know for sure what it is. Personally, my hearing isn't good. I've often asked someone with good ears to help me locate and identify sounds that are otherwise mysterious to me. In any event, I never leave dripping sounds alone until I know what they are.

If the water is getting past a new flapper, it's either A) flapper does not fit, or B) the seat is bad/scratched, whatever. Maybe you're using the wrong flapper. The old American Standard toilets use a rubber flapper that a little bit shorter (shorter distance from "ears" to center of flapper). Another alternative is to spend $12 and buy Fluidmaster's flapper w/ seat repair combo kit. It installs over the existing seat with an adhesive ring that comes with it. Follow the directions exactly to orient the thing since it's a bit counter-intuitive, i.e. the hinge ends up "lower" than you would imagine. Works great.

I would consider getting a real plumber instead of a wannabee con artist. Codes have prohibited the use of PVC inside a structure since the mid 80's. When connecting PVC to copper they must use a copper female thread adapter and a PVC male thread adapter. Code expressly prohibits any female threaded PVC fittings. PVC should never be used for hot water under any circumstance because PVC is expressly listed on the pipe for a maximum safe working temperature of 73degF. PVC must be supported within 1ft of change in direction and at not more than 4' intervals however the hangers and supports MUST NOT restrict movement as PVC has a very high coefficient of thermal linear expansion. For runs exceeding 40' it requires expansion turnouts.

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.