Hey Claire,
Without seeing the sequence it is difficult to visualise.
I would suggest you look (again, sorry) for following:
Rogue keyframes – sometimes if you have 2 keyframes in the effect panel very close together, you won’t notice the “rogue” one (Zoom the whole way in to investigate).
In your nested sub-sequences, has the clip used, been split or similar?
Same goes, which is one that always catches me out, is where a clip in a sub-sequence is not extended to the length of the clip in the master sequence. Could be something like a transparent layer that remains at standard length.
Finally, is there any other effects on that specific footage that might impact the effect used – maybe try an switch them off one by one, to see if that changes anything on that section.
Including checking whether blending modes has been changed on any of the clips for that part of the sequences.
I know, you have probably tried all of the above.
But always worth repeating, as you can fault find 20 times across the same space, and still not see it before it suddenly pops out – that is my world 🙂
Good Luck
Mads