I would have someone come check in it person. There are a lot of "could be" here that a person wouldn't be able to really help you on Houzz but will have to see it in person and check all the possibilities. Possible that if removing your fixtures they wont find the problem and would need to open ceiling or walls to find out.

It could be the toilet or if you have any plumbing running through the floor but all the other facts that you're telling are saying it might not be that.

Have someone check it out as soon as possible and I would recommend not to use the bathroom in the meanwhile because the problem could get worse.

Everything is brand new on our roof, even tore off the old shingles. We actually used to have a leak in our kitchen around a vent.

But how could a roof leak cause an inch of water to collect in a bathroom, without any wet walls or wet ceilings on the main floor?

Our Kitchen/Dining/Living room are all open floor plan, with no interior walls anywhere near those ceiling leaks.

My husband will go up on the roof and into the attic tonight, and tomorrow will most likely be a call to a plumbing investigator.

With water, the sooner you investigate the better.

With water inside the vanity, the water is coming from the vanity plumbing:

- the sink, the drain, the trap, the supply plumbing, etc...but you have a rather excessive amount of water, and most of those items will leak only during use.

OR

-with the heavy rain, the vertical vent pipe in the wall could have acted like a conduit, with water streaming down the exterior surface of the pipe via surface tension. It could have come through the wall and into the vanity where the vanity DWV plumbing connects to the vent stack.

It's not THE answer. Just a possible idea. Heavy heavy rain, in conjunction with a recent new roof. I figured it's a possibility worth looking at.

The odd thing with that is the delay between the rain storm and the water showing. I could see water infuiltration from a roof leak indicating several hours to a day later. But several days later? That's why it would have been best to get into the attic as soon as possibly, before a drying cycle could occur.

I don't have a singular answer, just offering places to look at.

Best of luck as you try to find an answer.

my husband got up on the roof last night. Everything looked good, but he caulked/blackjacked around all the vents again anyway.

Then he went into the attic--again everything looked dry.

Went into the basement, nothing is getting worse, just drying out. He punctured a hole in the insulation plastic and let it drain.

In the bathroom, we did the food dye test. immediate leaking, like we thought. He had purchased all new toilet tank "guts", but ran out of time to install.

There was no water "in" the vanity. Our vanity has only drawers, and I fully expected to pull out drawers full of water, but dry as a bone. (the drawers curve around the pipes) https://www.menards.com/main/bath/bathroom-vanities-cabinets-mirrors/vanities-with-top/ove-d-eacutecors-32w-x-18d-white-brooklyn-vanity-and-white-porcelain-vanity-top-with-integrated-sink/brooklyn-32w/p-1488352854589-c-8402.htm?tid=-882706052094605830&ipos=21

The wall behind the vanity was dry. It sits flat on the floor, and the finish on the bottom is all split and cracked. This is why we think the water was deep for for a bit.

In the meantime, I am constantly checking everywhere to ensure that there is no water under the other bathroom, and checking all walls and ceilings.

We always blame odd things on "Casper"...

Ah, my misunderstanding. When you wrote that you pulled out the drawers to the vanity and the vanity base was split, and the bathroom scale had water in it, I though the scale was in the cabinet under the vanity, and the "floor" of the vanity was split from moisture, meaning there was moisture inside the vanity cabinet, under the sink.

That's why I thought the water was coming in underneath the sink in the vanity cabinet.

<sigh> lol

I was just trying to show that I had already done some pre-investigation, not the "I'm a girl, I don't know anything, please help!"

but all we can do is laugh and try to figure it out... if you're familiar with Christmas Vacation

(Todd is my husband's identical twin brother's name!)

No worries, you did well! I simply interpreted what I read incorrectly.