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So, I missed one of the endings, the one that apparently comes if you reach the top of the Abyssal Tower without fighting the Garm army, so I tried to use the plot jump feature to get that ending. Unfortunately, I wasn't able to get it because of some bugs.

So, what I did was the following:
* Plot jump to Abyssal Tower (the second last entry on the list)
* Went into the ice cavern
* The cutscenes that normally only happen on the first visit happened. (This is the first bit of behavior I consider a bug; the plot jump should really have marked those cutscenes as already having been seen.)
* I ended up being sent back to Ame, with it being night, and the exit being blocked by doors.
* Normally, you would get past this by talking to the innkeeper to get a room for the night, but the Call item that plot jump gives you overrode this, meaning that I could manage my party but not actually leave the town. (First major issue)
* Fortunately, I was able to call the airship to get out. However, it's no longer possible to enter the town.
* So, second trip through the ice cavern. No cutscenes, but the door at the end doesn't open, preventing me from reaching the Abyssal Tower.

As a result, I was unable ton continue the game from this plot jump point, and unable to see the ending I missed this way.

(My suggestion for fixing this: Make it so that, when the plot jump menu is used, that the flags for every mandatory cutscene up to that point in the plot are set, so that cutscenes for earlier parts of the plot don't happen again.)
[Should've seen this sooner, sorry].

I've gone and made an update that should fix the various issues you had here.