I agree with Bobby, this may (hopefully) be the cause, but if so it just means that you didn't design in an adequate way to fill the coolant without trapping air. You would hate to have to do a coolant-prep flight every time you wanted to drain and refill the coolant. (but not the end of the world).
I originally designed my system like Ed's. Minimal drag (just the 2 stock RV-6 inlets) but cooling was like you and Ed describe... OK, but you always have to keep and eye on it and often reduce power or AOA in order to keep coolant temps in check. Then I made a major change to provide TONS of air to an adequately sized radiator. Since, I never even think about cooling. Yes, I do probably burn a little more fuel but it is well worth it to never worry about cooling again. Its not rocket science. Adequate air to an adequate radiator equals adequate cooling. Change adequate to plenty in that sentence and now your are rocking!
Dave Leonard