The rules said that the time ends once the flag begins to raise but my run got taken down even with that because my bunny didn't stop does it count?

well, the rules said the timer starts on the level fade in and you had to record the level transition, your runs didn't had any of those so we rejected. However we saw a lot of players making the same mistake, so we are changing the rules of the yeah ILs to start the timer on the first frame of the bunny running animation on glitchless.

once we do that, we will re-evaluate your runs :)