I submitted 2 runs on Glitchless but my slower time is the one on the leaderboard and my actual PB is considered obsolete. Can someone explain or fix this please?

your faster run is obsolete, because you didn't put in a time without loads. Runs that only have real time are automatically ranked under runs that have ingame time specified.

I'm assuming you don't have a time without loads for your run, so just edit your faster run and put in the same time in the "w/o loads" field.

If you want to have ingame time for potential future runs, consider setting up livesplit for automatical load removal.