I tried pulling both the perk mod and toolbox off and re adding them and trying a verify file attempt to see if one of those would fix it but no luck. I remember one of the options I thought being able to un hide the perks in the soldier ability lists and had kinda wanted that enabled so I could try and plan out my soldiers more with the new classes.

I initially saw that as well, then it disappeard never to return.

Hopefully the devs are aware and will fix?

I'm not sure. All the base toolbox options are there, but the few additions that the perks mod add have vanished. I'm tried repairing files removing folders to have the game replace them on a load up and no go. The only mods I'm using are mainly the long war ones plus timer tweaks, retroactive warfare facility and I had quickstart as well

Hi, thanks to the user FreedomFighterEx at the XCom subreddit, I managed to get the Perk Pack options menu back:

You need LW toolbox for that. It doesn't work with Quick Start mod since it skip the first mission which made toolbox unable to initialize itself. Save and Load do fix the normal toolbox option but not for perk pack."

https://www.reddit.com/r/Xcom/comments/4ulf93/view_perks_for_long_war_perk_pack/


The culprit is the Quick Start mod. So I disabled it, started a new campaign, done Gatecrasher and the options menu was there! I hope this helps you guys! =D

So it was the Quick Start mod, for some reason I suspected this one, kind of a bummer I can't fix it without a new campaign as I just started a fresh campaign after Shens Last Gift and have invested a good chunk of time in it to not want to rush a new start.

Still, good to know the culprit has been discovered so I'll be prepared for it the next game I start up.
Much appreciated @Gus