The only explanation of this I could found is that "349" appears at frame, when warp zone re-loads, so that makes game to set "350" time unit again. It's really fun.

I would find this similar to smb3 pspeed vs timer (as I call it) where when you get pspeed in a level you fly through it, and the timer slows down to a crawl.

For example: In 1-1 if the timer stayed at the same speed all the way through the level as when mario first appears in the level, I'd say the final in-game time would be somewhere around 283. But instead with mario going really fast the timer slows down and you can get 294 max for an in-game time.

But we're not talking about smb3. Anyway I think that when you slow down you probably slow down the in-game time too (while running).

Probably since the game is used to mario go at running speed and with everything in the game going fast for mario to sucessfully complete the level at running speed at all times. So when he slows down after running, the game probably isn't used to mario walking, so everything in the game slows down too. And when I mean everything I mean like the timer and jumping physics. I'm probably completely incorrect on this though.

@Mars02 It doesn't seems to be something like that, it never happened in different places. This is maybe specificy of world 2 warp. And of course not similar with smb3. It never happened if slow down in another levels.

Looks like a case of the timer not updating visually.