Yeah, Burton boot and binding compatibility is a given. There's a Burton binding rep who posts here frequently. He could provide more info if he pops his head in here.
I have similar issues with my Flux SF45 bindings and Thirty Two boots on my freeride board. The heel area back of my boot is too wide and I have really jam my boot in to get it to fit and then do a penguin walk for a bit and only then can I fully tighten the straps. It's a real pain the ass to have to do this everytime I get off the lift. Size 9.5 boot - medium binding so not sure why this is case. Luckily I don't have any pain from it though.