My knowledge of layered images are limited but I did know a plugin that used it to make eye blinks work. Not sure if it's applicable to lip flaps but it is possible (though some python was involved)
momoplays
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https://drive.google.com/file/d/1vKiHhnhVPRcAF_f98zCb3PUqa3fCgAM9/view?usp=drive...
here's a renpy project stripped of everything to make sure there's nothing else that might be the cause.
transform enter(p=0.0):
alpha 0.0
pause p
easein 1 alpha 1.0
transform leave:
on hide:
alpha 1.0
easein 1 alpha 0.0
screen choice(items):
style_prefix "choice"
vbox at leave:
for n, i in enumerate(items):
textbutton i.caption action i.action at enter(n*0.75)
and code case you need it
I'm not sure if it's on renpy or your template file, but I recently discovered a bug that causes the first choice in an enumerate to start glitching out before resuming as normal. This doesn't appear to happen in a normal renpy project. As of writing, I tested it on both the stable release and the current nightly (8.3.4). This only happens on the nightly build but stable is working fine, at least for now.