I don't get ANY air in my counterflow unless I have a vacuum leak (due to the pump).
My set-up is like this: Kettle's valve -> 3/8" braided hose -> counterflow inlet (run upwards to outlet) -> counterflow outlet -> 5/8" braided hose -> Pump in -> Pump out -> 5/8" braided hose -> 3/8" ball valve -> 3/8" hose into the fermenter.
To sanitize + prime, my procedure is this: I fill a 5-gallon bucket half-way with a mild sanitizing solution, and I use a spray nozzle that I attach to the garden hose. I insert that nozzle into the 3/8" braided inlet (the one that attaches to the kettle's ball valve), WHILE under the water level in the bucket, and I push water through the hose until no more air bubbles come out. I leave both the 3/8" input and the 3/8" output in the sanitizing bucket, and I let the pump circulate this solution for 15-30 minutes, until I am ready to chill.
When ready to chill, I close the 3/8" ball valve on the outlet (circulations stops), then I put my thumb over the 3/8" inlet, and I attach it to the kettle's valve using a hose clamp.
Then I start the flow of cold water, and I open the kettle's ball valve, and the 3/8" outlet ball valve, dumping into the sanitizing solution bucket, until I get a clear running of beer coming out of the outlet.
Then I throttle back the 3/8" valve until I get the desired temperature.
When I'm done, I use the same nozzle to rinse out the chiller.
M_C