For what it's worth, my Bullfrog R8 air locks in pump 2 every time I drain and fill, regardless of whether I fill through the filter intakes or not. Am I correct in thinking the two intakes under the two filters are each feeding one pump/the jets that pump drives each? Because regardless of which intake I put the hose in, water only comes out through the jets driven by pump #1 (the one I never have a problem with).
In any case, on 2 fills the air eventually worked its way out by stopping/starting pump #2 over and over again (to the point I was becoming concerned about running the pump dry). On my third fill (yesterday) I had to bleed the air out on pump 2 as the OP did as stopping/starting just wasn't getting it done.