thanks, sorry for the late answer, i actually got an answer from a PM over at CR so i didn't check it in here.
I got that when i manually inserted the smaller arm9 (by compression) in to the AAI2 rom.
Well, what CT2 does when you say yes there, it's not only changing the size in the ndsheader but change a view bytes.
Addint to that it will "watermarking" the rom with "Crystal Tile" in the Chinese version 2 rom name in the banner.bin.
Anyway, if you are already looking at here, is the CRC16 function at gbatek wrong or it's normal that the CRC16 of the ndsheader doesn't match (in an original dump) or did my programmer do something wrong??