Not sure if this will work but it might be worth a try.
When I was working on my 100% -- I was doing street races and I found when doing the last street race that it would not "complete" if I failed it and used the "retry"-- the check mark would appear on my map but the stats and social club would not show it as completed-- I had to pass from a fresh reload to get it to register.
It is possible that this is occurring with the jumps too (although I am relatively certain in my case that I "retried" at least a couple of them).
Anyway-- it might be worth a try-- just go up to each one and do a quick save before trying them again.
I would make sure I don't miss any of the "checkpoints" also.... perhaps that's hanging you up.
Anyway-- just throwing this stuff out there-- hopefully something makes it pop up for you... this has got to be frustrating..... I'm at 96% myself with just Triathalon, knife flights, under bridges, & 5 jumps left for 100%---