there a slowdown in this part:

Too much enemies I guess. Try removing the hammer/fire/boomerang/whatever bros.

(Even if it's not the cause I'd remove some. Too much enemies is probably annoying. And I'm not sure if the hidden star there is a good idea either)

ok now test

It has too many sprite.
I made a area, and 120 1-way door in it(what the........)
And when I played with it, the timer-speed was very ve..eery vvvvv.ve....eerrrrr.....ry zzzzzzzzzsssssssssslllllllllllloooooooooow
So I deleted it, and Althing are running in normal speed.
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NSMB6: Beta Testers Wanted!!!

Yes. Its obvious. There are too many sprites, not to mention the hammer and fireballs the enemies throw.
I wonder, what is the limit of sprites in the screen before the game slow downs?
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Yeah. I guess that those hammer/fire/whatever bros are heavy on CPU because they're 3D models.

Also, for testing your hacks for slowdown, do it in a REAL ds. Emulators are not good for emulating CPU time accurately. Latest DeSmuME SVN with "Enable advanced bus-level timing" is the most accurate, but still not perfect. Emulators tend to tolerate CPU overload more than the real thing. And to make it worse, it depends on the computer you run it...