A single toilet can waste well over 1,000 gallons of water a day in 2 scenarios:
1. Float shutoff valve is faulty and continues to fill water into the overflow tube even after the tank is full
2. Flapper valve sticks open and the tank won't fill because the water runs into the bowl. Or the flapper doesn't seal properly and the bowl keeps refilling every few minutes.

Either of these problems can occur intermittently, so you may not have noticed. Monitor your toilets closely each time you flush. Listen to them fill and shut off. Open the tank and look inside as you flush to watch the working parts. Does the flapper ever catch on the chain? Is the water level all the way to the top of the overflow tube when the tank fills completely? Do you ever hear the toilet fill itself a little bit for no reason? If any of those occurr this can waste an incredible amount of water.

Once you rule out the toilets, you can pursue the utility company for a refund.

1. They changed the meter and somehow screwed up the numbers.
2. they mixed up your meter with a neighbors.

Steady. You will prevail in the end. Something's obviously wrong. They'll get it before its over.

I will agree with aidan_m (above) that a simple little toilet leak may cause more financial grief than you would expect.

This is usually caused by a worn out flapper valve or faulty fill valve. Either way, these are very inexpensive items that you can easily change yourself in 15 minutes or less.

By a Fluidmaster 400A and a universal flapper (unless you have a unusual toilet) and follow the directions on how to change.

If anything, you toilet will benefit from a nice tune-up.

When EBMUD came out, no water was running! That's what's so confounding--a 1,300 gal/day flow stopped without me doing a thing, except I'm still 40gal/day over my average, but that could be the carry over from the flowing period.

So there's no leak now, and I simply can't imagine someone stealing that much water without me knowing it. They would have had to do it from the front of my house.

Put a few drops of food coloring in the toilet tank and watch the bowl to see if the color shows up.

If the color gets into the bowl, and it may take a while, then the flapper is leaking.

what was your meter reading 6 months ago? and today? the city keeps track of monthly/yearly usage. there should be a meter reading from 1yr ago, 9 months ago, 6 months ago and so on. mine is billed every 3 months. have the city tell you what the reading was for each billing period for the last year?