FF3usME dialogue editor broken?

I have seen this before, too, under similar circumstances. There is definitely a bug. In my experience the risk seems to be if you are working with expanded dialogue, save, continue editing, and save again.

Nowadays I do all my dialogue editing in the exported script file. Any time I import changes into FF3usME, I save and immediately exit. That seems to avoid the bug, though it may be overkill.

As for recovering your ROM, I am not sure. Have you been keeping backups?
If all the caption pointers really are corrupt, then you may be in for some manual recovery fun time. I will see if I can figure out anything about this bug, though. (Has anyone investigated this already?)