Ok, now I'm starting to think it might not be a silly mistake on my part but an actual problem.
Just played a couple more short sessions and they are recorded. You can also see that the two missing sessions are recorded here, but has 0 hands for some reason. For some reason all the hands (1900'ish) of those two particular sessions seems to have been filtered out. Although the session result graph have them registered.
The hands have been imported though, as evidenced by the fact that they do show up in the "Player Statistics" window.