They do! When there aren't any changes, it doesn't seem to happen, but even little things (how far eyes are from the bangs/ears) crop up, and when you work with the sprites for long enough they start standing out.
I haven't had a chance to try out the eyebrow adjustments from the latest version, but this has pretty consistently been a thing. From what I can see in the current stable build, it seems like there are two "groups" of faces: ones that match Standby, Hands on Hips, etc., and then ones that match up with Both Hands Raised, One Hand Raised, etc. When you take a face you've customized more from the former group and change its body to one of the ones in the second, that's usually when I've gotten that to happen.
If you want I can boot up the stable build and put some other examples together for you!
Also, on an unrelated note, there seems to be a minor bug with the SVG exporting:
I exported about ten expressions individually (not as a batch- it got through five expressions in a batch export then froze up and stopped working) but they all seem to have this same visual error. The image quality also seems to have suffered a bit compared to the stable build's SVG exports.
