When your seat lands back into the tack while in the rising trot, you could be effecting your horses back.
The purpose of the rising trot is to free your horses back, so when you land back into it for that breif moment, that could be effecting his/her movement.
Your heels are meant to take your bodies weight, to secure your seat and your lower body
I do not ride with my upper thigh, and my knees are always open *not gripping the saddle*
I ride with my heels taking my weight and my inner calf around my horses girth.
I am not saying that you post from the stirrups - but your heels should be taking your bodies weight - because they anchor you and aid you. When you grip with your knees or close your thighs, you effect your seat and you effect the flow that should be dipursing into your heels.
Leg position is imperative. Your legs must aid your seat, keeping the impulsion, and aiding in lifting the back and ribs. You do that through your lower leg, not upper.
The post must be a soft, gentle movement. When you allow your horses movement to lift you out of your tack, there's not allot of work that you need to be doing.