Why are some of my text boxes not aligned to the baseline?

Perhaps it wasn't obvious from my first post, but I only have two typefaces throughout the document. The text boxes are copy/pastes of each other, and I have not changed the settings (as far as I'm aware, unless there's an accidental keyboard shortcut way to do so).

My problem is that somehow, in some of the text box pairings, the text has become unaligned, while in some it remains properly aligned (as shown below, these are two separate instances of the text box pairings on the same page)

What is your first baseline setting in area type options? If you want it the same across typefaces it needs to be Fixed or Leading.

This is a font editor:

Font size is the height of that box. The font designer can place the baseline anywhere inside that box. 

Various typefaces will differ on their own built in defaults of line spacing. One solution for this is to set up a baseline grid in your document and have the area text boxes set to align to that baseline grid.