I wanted to share an issue I had and how I fixed it, in the hopes that perhaps a bug can be found and fixed.
I experienced a probably difficult-to-reproduce issue where Maplex labels for a few (but not all) of the layers in my layout did not render correctly in PDF exports only. Live display of the label and exports to JPG were correct. The text appeared to draw at one character spacing, but the halo drew at a different character spacing. I think I've seen this happen before. I happen to have several similar layouts, and even one at the same scale using the same font, but did not experience the rendering issue in every layout.
I tried many things to see if I could eliminate the issue. Finally, I found that changing the orientation of my layout from portrait to landscape and then back to portrait fixed the issue.
Previously, I tried the following, and none of them fixed the issue.
The font is a proprietary font owned and developed by my organization, contracted by a font foundry. Because of the proprietary font, I do not feel comfortable sharing that font file or this layout for testing. In fact, I've saved over the layout, so I probably wrote over whatever was causing this anyway! I've experienced issues with this font in Acrobat's Preflight analysis. It always identifies that all text from this font has invalid glyph widths, so perhaps it contributed to this issue. Once again, the halo issue was unique to the one layout I was working with.
Hmmmm...this is an interesting one especially using proprietary fonts. The closest bug I found was BUG-0001161138 - ' When enabling halos with letter spacing and exporting to PDF on certain fonts in ArcGIS Pro, the text and the halos do not coincide when the letters 'f' and 'l' are together" and only affects Calibri, Constantia, Yu Gothic and Yu Gothic UI fonts.
So question for you - you mentioned it's only seen on a few labels. Do those labels have letters "f" and "i" together? I know it's a long shot...