This is because the theme is using an animation and not a transition. And animations get started once a widget gets shown.

I don't actually know why we're using not using transitions here?

Well a transition is just a cross-fade, too limited there.

You're just doing a cross-fade in the animation?

Benjamin, nope I'm doing all sort of nasty things as usual, anyway this issue seems gone here, Allan?

Whats nasty about this ?

@keyframes check_check {
  from { -gtk-icon-transform: translate(6px, -3px) rotate(-45deg) scaleY(0.2) rotate(45deg) scaleX(0); }
  to { -gtk-icon-transform: unset; }
}

Matthias, well it's quite a bit of stuff, legit but pretty complex.
The issue is not gone thought :-/

I tried working around the issue by setting the -gtk-icon-transform prop in the the normal state and unsetting it in the checked state, but it doesn't work for indeterminate check and radios and it's a hack anyway. Moving to gtkstylecontext since this issue can't be tackled within the theme.

I think comment #1 has all you need to know: use an animation, not a transition. The transition works according to spec...

uhm, animation triggers on show, not on state changes so I can't use those, I think I found a way using transitions though, the downside is that thre's a longer (normal) transition when brought back from backdrop, but I think it's a minor offence wrt animating on show. 
Fix pushed with commit 15b2dbf9a8e6de17fb74eef989ed5923ef6c6180 closing.