I have this problem with my new streetkid playthrough. Nomad which i started yesterday has no problem with that - i didn't do any side missions with streetkid though - maybe a trigger (the gun quest wasn't it)
wow this is dumb - someone found a way...
In the meantime i figured that i did indeed couldn't raise stealth due to lack of level - also that i need at least 1 on cold blood... but after a full shootout with 6 Tiger Claws i couldn't get 1 (!) XP for cold blood.