Are you playing the latest version? This was recently fixed in the 26.9 update, according to the changelog: * Player Perks added by mods now properly show up when leveling up, instead of needing to reorganize the list first.
I've relayed the issue to Threshold who will look into it.
On the plus side, the issue with the Perks not appearing is caused by them being new additions compared to older versions of the game. So once they appear, there should no longer be any issues with them being invisible upon further level ups.