I had the same problem with my Edelbrock intake.One of the holes that the thermostat bolts to was not drilled and tapped deep enough.I had to get a shorter bolt,and the problem was solved.
UPDATE....... I used a different OEM T - stat housing and added a few washers to my stainless steel hardware and no leaks. I noticed that when I bought my intake used that the upper bolt was drilled and tapped for a bigger size. Maybe it wasn't deep enough, maybe there was an issue with the thermostat housing, IN EITHER CASE IT DOES NOT LEAK ANYMORE. Now Ive got to pull my engine back out to fix a bottem end noise and send the heads back to Gunner at Patriot Performance to have the valve guide seals replaced. These things I didnt realize after I fixed the coolant leak and got to drive the car to break the new rings in. Oh well tis life....the woes of a project, time and money.
Hell, I never thought about the bolts bottoming out. Good idea with the washers. Actually, I might just try that with mine this weekend and see if maybe that might be happening with mine, by chance. It's a stock intake and housing on mine, but maybe there's some crud in the bolt holes that I can't dig out, and it's not letting the bolts torque down all the way...