AAARRHHH! I honestly dont know WHAT it could be then! I've got a feeling its just the Skingrad gate or the whole save is infected no matter how far back i go >_< i dont what to clear the cache because that causes all sorts of problems with DLC resetting on other saves aswell doesnt it?
i don't think it does.. or at least i never experienced a problem... and i played oblivion and both fallouts and all of their dlc with no problem.... and i was reseting the cache every few hours... if i didn't, the load times would keep taking longer and longer...
also, if you try what i suggested, maybe you could also try going into a completely different oblivion gate first before going into the one you know your having problems with.
and i don't know what causes this but i do know that when it happened to me i was doing oblivion gate runs.... and after i grabbed the stone i would jump off the platform to work on my acrobatics... so i'm not sure if somehow my actions during that brief fiery scene somehow corrupted my save so that every sigil stone loaded as "already grabbed".... so i told myself next time i do try to play through, i'm just going to stand and do nothing after i grab the stone....
man this annoys me to even think about... i feel your pain...