I've run 3.9.9 and it's doing the same as 3.9.8
The Pre-Scan says no Reparse Point Problems but underneath it says it has found 73 and when you hit the repair button and it does the scan, nothing comes up with it saying at the bottom, Problems: No but for Info it reports 73.
It's as if it's ignoring non-system Reparse Point corruption.
There doesn't appear to be any adverse effects, but it makes you wonder what is wrong with the ones it reported previously.