Not certain if you changed the scale of the clip using the Effects Controls or not, but I had a 24hour boxing match with PPCC. Timeline played perfect and export showed extreme flickering on one segment that was iPhone footage at a basketball game. Everything I tried from every forum only changed he way it flickered.
The Solution: I removed all Effects and started over. Rather than scaling the clip in the Effects Controls to fit the frame I right clicked the clip in the Timeline and selected Scale to Frame Size and voila! Houston we have a solution!
I’m sure all you pros out there know this, but I’m a noob and I’m sharing this for noobs.
Hope it helps.