Depending on the structure of the query, the placement of the NSQL security join can influence results too.
Assume you ran this code
SELECT object_instance_id FROM odfsec_project_v2 WHERE user_id = USER_ID_HERE
Try running as different users, ideally an admin for starters to rule out first suggestion
Since I don't know your rights model and have no access to your system, it's a bit of a guess right now
I'd start by taking a user with no result in that query and granting the "Project - Edit Management" right on the project missing, if that works then re-examine the rights model. In particular OBS.
One other thing to note is the full view is not correct in 13.3. It shows users users who don''t actually have access due to a problem with some of the rights.