Yes, exactly. Each individual font file that is exported is an instance.
The measurement stuff is all when you’re in edit mode (i.e., when you’re editing a glyph): if you select a path or node, the Info box shows you the size and position of what you’ve selected. This is often very useful, to make sure straight lines are actually straight and so on, but I don’t think it has any relevance to your incompatible glyphs.
The most important bit in the thread I linked to is in Georg’s first answer: You need to make sure the instance and master coordinates match – even if you don’t plan on interpolating (i.e., making a variable font).
In other words:
- In Font Info > Font, you have to make sure that there is a weight axis.
- In Masters, each master should have a Weight entry under Axes Coordinates.
- In Exports, each instance should have Weight entry under Axes Coordinates that is identical to the entry in the corresponding master.
Does your font have all these things correctly set up?