I’ve been working on this font for a client and for some reason when I export it seems to confuse X-height with Cap height. Or rather the Ascender.
This makes the font stick its head above the text field when testing it in Illustrator. In Glyphs, it looks fine, with plenty of space between cap height and ascender, but when exported it seems to put the X-height as the height of the type, and not the ascender. I have no idea why, it has never happened to me before.
Illustrator calculates the first baseline by the height of the shape in the letter “d”. You might need to put a tiny shape at the ascender height in the “d”.