Maybe it is because the #POPUP line is blank?
I haven't tried editing decisions in SC3, but in SC2 a blank #POPUP line designated a dummy event that could fire in the background but wouldn't be visible to the player. Of course, #MESSAGE didn't exist in SC2 so something might have changed there.
Indeed, I've always used POPUP before too - for this campaign, I've tried both POPUP and MESSAGE without success. This is where new scripts from the new official campaigns use the <<TAG_NN>> syntax. <<TAG_NN>> seems to remotely reference language text entries (English, German, etc...) in separate text files. I've fiddled with that too, but I'm not sure I'm doing it right or whether we even need to. I was hoping I could just do it the old way without the <<TAG_NN>> entries. I'm doing it "the old way" in other non-decision events, i.e, not using the <<TAG_NN>> syntax and putting the English text directly into the script.
OK I've looked through the Storm over Europe campaign and think I've figured out how the tag thing works.
In _1939/Storm over Europe/Scripts/Events there is a folder for each of the games languages (DE, EN, ES, FR). Each of those has a bunch of text files corresponding to the different script types. (I've copied the one for 'VICTORY' scripts below, simply because it is the shortest.:
<<TAG_1>>= AXIS MAJOR VICTORY
<<TAG_2>>= AXIS DECISIVE VICTORY
<<TAG_3>>= AXIS MINOR VICTORY
<<TAG_4>>= ALLIED DECISIVE VICTORY
<<TAG_5>>= ALLIED MINOR VICTORY
Seems to be a localisation file, where an event with text '<<TAG_1>>' will show up with whatever text is listed here, using the set of tags from whatever language is selected (so if the required cities are captured for an Axis Decisive Victory, the same script fires regardless of what language is chosen, but if english is chosen it shows up as 'AXIS DECISIVE VICTORY' but if german is chosen that same script appears as 'GROSSER SIEG FÜR DIE ACHSENMÄCHTE'.
If I'm right about that, then your decision script would need to have
Then create the folder EN in <your campaign folder>/Scripts/Events, and then create decision.txt within that, containing the following:
<<TAG_1>>= Shall we support the Sapien Brotherhood?%N%NYes or No.
If it's not something simple (like POPUP or TYPE mentioned above) I suspect this is where the problem lies. Nation 53 (The Sapien Brotherhood) is a new nation created during the game at 50% mobilization towards side 1 (Terran Empire) using a mobilization-3 script. It is given control of a couple hexes with territory scripts. Those seem to be working fine as far as I can tell and the Sapien Brotherhood shows up on the war map and in the diplomacy list as expected. (I can post those scripts later if it would help. I'm at the wrong computer right now.) Once nation 53 exists, the Terran player should be given the decision to support it or not, but that script (listed in orange above) refuses to fire.
Is 53 created out of a territory script purely, or does it partly exist on the map beforehand? Because I'm not sure if Territory scripts by themselves can (properly) 'create' nations, only add to them. Again speaking from SC2, I tried this at one point and the nation appeared on the map fine, but it had a war entry script meant to bring it in as soon as it was created, and that never fired. If I used the other side to declare war on it though, then it would enter.
To solve that I used a Surrender 1 to create the nation instead, although I'm not sure how well that would fit your campaign. Those fire instantly after a nation surrenders, and you could use a surrender 2 to force-surrender a nation to create this new one.
...Although, you said that the event would fire "right away", which I take means Turn 1? Because if that's the case, wouldn't it be easier to just have 53 on the map from the start? (Perhaps with a popup that says 'Look, these guys recently got created'?)