Hello Geez,
I just tested it a bit more since I wanted to be sure. The double animation happens for pretty much every item. Throwing a gun while crouched makes you stand up before trowing. Any other item makes you play the standing throw animation after throwing the item while crouched pretty much every single time.

I also had a few cases where an item disappeared after multiple attempts and at a certain point I got the reverse effect (Standing throw followed by crouch throw) but I think that was just a little desync, as I crouched first when I vaulted right after.

Hope this helps.