Landing with both feet on the board even if it's upside down after half a flip means you're closer than on any attempt where you get the full rotation but only one foot back on. Doing the latter means you know how to fling the trick and safely 'simulate' it which works to first figure them out, but after a while one needs to come to terms with and accept the reality that they actually can do the trick for real (which is big and more meaningful in skating one might think at first) and thus adjust their parameters in order to get the jump right which is the hardest part.
If you catch the board with both feet, regardless of what the board did, then that means your jump is correct, and if the board didn't fully flip then that means your newfound correct technique for the jump is weakening your habitual pressure points. Should keep the jump and just adapt the pressure points accordingly with time, you'll naturally figure them out at this point. I think I can visualize what you're doing because I've seen so many people learn 360 flips and would (obviously, naively) recommend insisting with the big toe on your back foot really pressing down on the toe-side rail as you pop, and the front foot being lodged well inside the concave wherever you feel the tension from the back foot builds up further up the board. Essentially exacerbate your foot positioning a little bit and you're there, ready to request a user name change to I Used To 360 Flip Less.