ecobee3 thermostat on old 2-wire boiler
I was having the same problem...until I switched my multimeter to ACV!!!

I had purchased a fast stat common maker. I was measuring 12V across the thermostat terminals and R and C with my multimeter set to DCV, and wondering where I was going to get 24V from.  I found a 24V DC transformer and hooked that up to R and C thinking it would work but of course, no.  Honestly, I played with it for hours, then it dawned on me that I must be doing something wrong.

Nothing was working, ecobee wasn't happy.  

Switched multimeter to ACV, and found that lo and behold, R and C on the boiler does give 24V.  rewired everything and from then on everything worked perfectly.

good luck!