Thanks to everyone who has responded.
in hindsight a picture WOULD have been brilliant, but i didn't think of it at the time.
to clarify a few points:
The seal was just over the size of the flaps grommet.
and the red thread WAS pretty long, the seal could flop about.
The seal was jammed IN the grommet WITH the closing loop (not IN the loop). and when i say jammed i don't mean external force, i mean that in pulling the pin it was somehow at exactly the right place to catch the loop and get stuck.
Unfortunately i don't have my rig (it's already gone for a repack)or i would set up the picture.
As for abusing/thrashing my rig, that doesn't happen.
My best guess (uneducated though it may be) is that the thread was longer than it should be and as i pulled the pin the seal was hanging/pressed right above the grommet and the thread was pulled through the loop.
Now i can't honestly remember if the thread was through the loop or not, but i think it was. either way, when i said i was going to check my pin before every jump, i mean that i will be looking for that seal and making sure it is as far away from the grommet as possible. your mind is like a parachute: it works best when open.