^^ ok well instead of sitting on my hands and pouting, I decided to do more google-fu. I found more people having issues regarding katie and zombies and her showing up after, and people having success if they themselves fought the zombies.
So I decided to load 3 days back and just fight the zombies myself, and see if I can get it to work.
Then I noticed something odd. When I did it over again, I ended up with extra journal entries / todo tasks. I then got an inkling. Many cavern plunders and panda pieces later, I have solved the problem.
I just posted the following in the bug forum, but incase someone sees this and not the bug forum (like I did to begin with) I'll reproduce it here
TL;DR:
If you did not kill the zombies (and therefore not get the key) and already have the map piece before talking to Katie at the waterfall, AND you offer to help her with the treasure BEFORE offering her the map, the quest will bug (Katie does not show at the skull door).
VL;WR (very long will read):
My hypothesis was that offering to help her and then the game forcing me to give her the map (rather than you selecting to give her the map first and then offering to help afterward) was causing the issue, as you don't officially get the quest (in your journal) if you offer help first. Further, When you offer the map and then to help, she gives you the option (skull or key) -- if you offer help first and are forced to give the map, she does NOT ask what you want to do, and you do NOT get the quest / journal entry.
I ran several paths of the quest to test each scenario, making sure to keep every other variable constant (have all the same items, make all the same choices in interim (e.g. feed the serpent, then free him and loot the ring))
(1) have the key - offer help and map forced
(2) have the key - offer map first and then offer help
(3) zombies alive - offer help and map forced
(4) zombies alive - offer map first and then offer help
notes:
*I already had the piece of map in my inventory for every trial, as I obtained it before midterm break (maybe this is causing the whole problem?)
*I already had the red gem as above
*I originally did scenario 3 the first time 'round (which I retested under stated controls)
*every scenario results in 1 journal quest: to help katie find the treasure. only (2) and (4) result in an additional entry (skull or key quest).
We'll skip (3) for this initial list, as that is where the problem lies
Scenario (1)
Offering to help first forces shawn to give katie the map, which results in (a) no second quest entry and (b) no choice of skull or key. However, as I already had the key, I headed down and grabbed the skull. Katie was waiting at the skull door.
Scenario (2)
Offering the map first and then offering to help her results in a quest entry (either find the skull or find the key - whichever you choose). I already had the key, and I chose to find the skull (because pandas). After obtaining the skull, Katie was waiting for me at the door.
Scenario (4)
Offering the map first, as above, gave me the choice of obtaining the key or skull as an official quest. I chose to obtain the skull (because, again - pandas). I got the skull, and Katie was waiting at the skull door.
Scenario (4b)
FURTHERMORE I did a side-test of this scenario to see if perhaps speaking to Katie at the zombies was an issue. After obtaining the quest for the skull, I did 2 parallel runs (one not going to the zombies to talk to her, and one going to the zombies and talking to her). Both scenarios resulted in success.
Scenario (5)
Huh what scenario 5? Well, there is an addition scenario I didn't run (zombies alive, offer map, offer help, choose key quest). But that would have taken me an additional hour at least, and I think I nailed down the problem in scenario (3).
OK SCENARIO (3)
As a refresh, this scenario is when you talk to katie at the waterfall while the zombies are alive, and you offer to help her before you offer the map, which forces shawn to offer her the map, resulting in her not giving you the choice to choose skull or key. Katie goes to the zombies by default, and kicks you out of the area. After obtaining the skull, she is gone from the zombie area, and does NOT show up at the skull door.
So to sum up
When encountering katie at the waterfall, and
shawn has the red gem, the map scrap, and does NOT have the key,
then offers to help her BEFORE offering the map scrap,
the game does not offer key - skull choice,
and ultimately results in katie bugging out.