I've been experiencing perk problems as well, but only on some maps.
Perks work fine on, say WestLondon. But if I go Farm or Bedlam they won't go up. Doesn't say they've been disabled, just nothing I do counts toward their progress on these maps. Exact same setting on both.
Edit: I went through all the official maps on beginner long with no mutators. Only Foundry and WestLondon let me advance perks. I didn't test unofficial maps except Waterworks, which worked, and LastStand, which didn't. Both whitelisted.