I stand corrected. After I tried it again, I was able to take the class with a sorcerer, but only as my level 10 class, although I fulfilled the requirements after level 8 (ie not as my lvl 9 class).
You have to actually be able to cast Polymorph Self when you level up to take PnP Shifter. Perhaps when you took level 9 you had used up all your level 4 spells, so you couldn't actually cast Polymorph Self, so you couldn't take PnP Shifter. If that was the problem, sleeping would have fixed it. That's not the way we'd like it to work: due to scripting limitations, it's the best we can do.
As for the Dragonfire Adept, it is possible to select Shifter, as long as you are able to cast 3rd level spells (I took levels as Sorcerer to do so), a requirement that I either failed to notice initially, or I did and thought that picking DFA would qualify me for it, as the Lesser invocations count as 3rd and 4th level spell (at least that's what the descriptions on the manual and in game say and Humanoid Shape counts as 3rd level spell, as is Warlock's Mask of Flesh), but I guess it doesn't work that way.
I'm pretty sure the Shifter description used to say "3rd level arcane or divine spells", but that must have gotten lost when I worked on the description a while ago. I'll fix that. In any case, that's how it actually works, so warlock invocations don't count toward the Shifter "3rd level spells" requirement. This means that a warlock needs to have an alternate form through invocations and also be able to cast 3rd level arcane or divine spells though another class. I expect the same applies to Dragonfire Adept.
In any case, I posted this because of my concerns that something had gone wrong during the installation. My original question is whether or not the DFA's Humanoid Shape is supposed to work as Alter Self, ie assuming a form and storing it, or just assuming the form, in which case the options and quickslots have no use being there (and if it's so, it is what misled me in believing that DFA can store his assumed shapes).
Sorry, I don't know the answer to this, and I'm not in a position to investigate at the moment.