After replacing a flapper valve in my leaky toilet, I made note of my water meter reading and went on vacation for a week. 

On return I found that I had used 100 gallons of water, about a half gallon an hour. I continued to monitor the meter and find this to be a pretty consistent phantom use. 

With no known water use I've done multiple tests, confirming that the water meter still advances.

I've confirmed that:

* Toilets don't leak (dye in the tank and pull the tube out of the overfill tube)
* Faucets and showers don't leak (even put balloons on the outside faucets and paper towels in the sinks)
* T/P valve leaks about an ounce every 24 hours (even while this is all going on)
* HWH drain is not leaking (dish under the valve exit)
* dishwasher and clothing washer haven't filled when off
* exposed piping is not leaking
* the ceilings where the upstairs pipes are located and the sill where the pipes go through the floor show no water or stains (and since it's been at least two weeks, I'd think such a leak would result in a collapsed ceiling by now).

I've even turned the HWH (AOSmith ProMax Direct Vent) gas off to see if water is leaking into the combustion chamber and instantly evaporating - after the HWH cools, there is still no water on the floor after the meter reads an additional gallon and a half use. 

I have none of the following:

* water softener
* ice maker
* humidifier
* sprinkler.

The town has checked the meter and says it's okay. Also of note: The problem is not constant, but occurs often enough that If I watch it, I can see the water meter advances and reverses. 

It will go backwards a few hundredths, then advance by a little more. Also, when the main valve is shut off, there seems to be no use.
Anyone have any ideas? 

EDITS/ADDITIONS: House has a basement. HWH is in basement. HWH has a small thermal expansion tank. Main valve and water meter are inside basement. Meter is a model Neptune E-Coder R-900. 

Last night I shut off the upstairs supply via gate valve so I know that any loss would be from either the first floor or basement (all pipes are visible) and turned off the gas to the HWH (so leakage into the combustion chamber wouldn't boil off). I'd think that if water is leaking into the HWH combustion chamber with the heat off, 3 gallons would show up on the floor or in the little sight window, at least. 
Results: 4 gallon loss overnight, no water on floor, no water visible in HWH through sight window at base. 

**Could it be that combustion chamber is double sealed and that water is leaking into the chamber but not to the burner or outside of the HWH?** 

For the next test, I shut off the water supply to the HWH (and the gas too for safety) and waited a half hour. Result was no metered use while the valve was shut, and an influx of about 1/10th gallon when it was opened. Normally I'd say this confirms a leak in hot pipes (there is none, everything is visible) or, more likely, the HWH. But, there is no leaking on the floor and nothing in the bottom of the combustion chamber. I called A O Smith and they advise me that any leak on the inside of the tank would drain to the areas I noted. So, I'm back to square one.

**Am I missing anything?**

Here's another idea...If my guess that it is a leak into the combustion chamber/flue of the HWH, and AO Smith's advice is misunderstood (the chamber will hold water) suppose I turn off the gas and let it sit for a long time, say two or three days. **If the flue eventually fills with water, will that render the unit dangerous?** I can use the HWH now, so if the leak is the issue at least I have some time before I have to replace it. If I trash it, it would need to be replaced right away.

UPDATED STATUS

The meter is about fifty feet from the HWH. I installed a check valve (yes, correctly) about a foot after (into the system from) the meter and checked overnight again. Now the meter reads about a tenth of a gallon overnight, or about one-one hundredth a gallon an hour - a 98 per cent reduction in "phantom water use" reported.

Could it be that the water in the house is either pulled out by movement in the main or is pushed out expansion, turning the meter backwards? And then, because the warmer exiting water has a lower density than the cooler exterior water reentering the house, could that account for the meter advancing more than it retreats?

I wonder if it is a coincidence that the plumbing between the valve and meter is about 2% of the distance between the meter and HWH? The later tests, with the check valve installed, would have been done with 2% of the warmer water (between the check valve and the meter) than was available before the check valve was installed (between the HWH and the meter).

Any Hydraulic Engineers out there know the answer?