My other char with a different prestige class had the same issue, as far as I recall. But I might be wrong about that, and the issue with the char in question might stem from having two prestige classes that offer warlock spellcasting progression.
I checked it on jegs, and a pure warlock got their Invocation Progression feats properly at levels 6, 11, and 16. It wouldn't be much of a problem, but
Essentially, you miss out on those extra invocations as what extra invocation feats are available to you is governed by the Invocation Progression feat and it hurts your build a lot.Warlocks may now select Extra Invocation feats. You may only select Extra Invocation feats for invocations up to one level below your maximum. This means you may select bonus Least invocations at level 6, Lesser invocations at level 11, and Greater invocations at level 16. Dark invocations can never be selected as Extra Invocations. Eldritch blast shapes and eldritch blast essences cannot be chosen with extra invocations.
Also, in case someone actually reads these, Hellfire Warlock abilities don't drain constitution properly anymore (I have a char bugged in this manner, used to work fine a year ago); and spidershape gives me 3-5 times my other char's hp for some reason, maybe some bug in the polymorph script fix. So there's also that.