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. 
Can you elaborate? The choice screen in this template is the exact same choice screen as a regular default project, just with the styling made explicit. You'd need to share this new enumerate and animation code you're adding and ideally how you're testing. I believe I recently saw an issue relating to ATL on the Ren'Py GitHub as well which may be relevant.
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