What kind of flat is this?
That looks like the sort of hole you get from tiny bits of glass working their way through the tyre, then slowly cutting into the tube. I'd check the outside of the tyre for tiny cuts, and the inside for barely-detectable points poking through.

This photo shows the sort of small cuts I'm talking about:



Each of those had a little bit of glass or something in it once, but most of those work their way back out. The problem is that the ones that don't usually work their way in instead. If you poke in there with something like the file shown (a sharpened spoke is what many bike mechanics use) you'll sometimes find a ~2mm or smaller triangle of glass. 

When those work through the inside of the tyre they don't punch a hole like a nail does, they slowly cut a little slit as you see above.

The way to avoid this is by going over your tyres every few weeks and digging out those bits of glass.

Note that even very puncture-resistant tyres will suffer this, just less often. I've had Marathon Plus tyres puncture this way, but only once (I use those tyres a lot). This guy had the same problem with tyre liners. Picking the glass out is the only solution.

Echoing @DanielRHicks comment: one annoying possiblity is that you have a little fragment of glass or something loose inside the tyre. So every time you check the tyre you don't find it because it slides around as you rotate the tyre checking it, and every puncture is in a different place. So check for that too.