Ok so I was right but it happens after a certain amount of HSD. The combo I used is with a Level 5 Frank. I used Team Bee to make it easy on me.
Instant overhead j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, S, j.S, j.QCF+H, QCF+M (Wallbounce) , QCF+M (No hard knockdown)
On shorter combos, you still get the hard knockdown though:
Level 5 Frank: LMHS MMHS qcf+H qcf+M qcf+M (hard knockdown) camera shot hyper.
I'm not sure why this would be different for longer combos, I always thought hard knockdown times were consistent.
EDIT - okay I landed the combo you listed and you're right it doesn't work. But you don't get a soft knockdown, he air techs before he even reaches the ground. You still get the hard knockdown for the first wallbounce though. I don't know enough about the system mechanics to know what's going on.
Some experimentation.
Instant overhead j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, j.QCF+M (while jam session is still out get wall bounce), grounded QCF+M -> get the hard knockdown
Make it a bit longer:
Instant overhead j.M, j.M, j.H, j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, j.QCF+M (wall bounce), grounded QCF+M -> get the hard knockdown
Instant overhead j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, S, j.S, j.QCF+H, QCF+M (Wallbounce) , QCF+M -> No hard knockdown
(note that ending with 2 qcf+M's actually gives you ~30k more damage compared to qcf+M hard knockdown into dp+H, but since you flip out you don't get a chance to do your hyper ... EDIT - yes you do, check below)
Cutting this combo in half:
S, j.M, j.M, j.H. S Call Jam Session j.QCF+H, S, j.S, j.QCF+H, QCF+M (Wallbounce) , QCF+M -> get the hard knockdown
So yeah, it's the hitstun decay.
AFTER THIS I'M DONE I SWEAR:
Instant overhead j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, S, j.S, j.QCF+H, QCF+M (Wallbounce) DP+H into tools hyper : 883300
Instant overhead j.M, j.M, j.H, c.M, s.H, S, j.M, j.M, j.H. QCF+L, QCF+L, S. Call Jam Session j.QCF+H, S, j.S, j.QCF+H, QCF+M (Wallbounce) , QCF+M xx tools hyper: 919300
You don't get the hard knockdown, but you can catch them with the Tools hyper before they flip out. ~36K more damage (I can't guarentee that one combo didn't get 1-2 more extra hits from jam session than the other so I can't claim an exact damage difference)
There you go my friends, real time Marvel investigations.