Thermostat housing leaking
I usually let the silicon "cure" for a couple of minutes before sticking it together. Waiting a while before running water through it is good advice also.
Not sure how it works on the cast intakes, but a lot of the aftermarket intakes don't have blind holes for the bolts, meaning they go through to the water.
I once had a leak I couldn't figure out until I put some teflon tape or TFE paste on the thermostat housing bolts. Now I do it every time.
If your bolt holes go through to the water, this may help.
Good luck
Steve