I asked this problem in a Avid forum and they tried to give some solution but none helped and they said to ask this problem in FCP forum.
I think you[Shane Ross] are right.Its how both apps read the DSLR footage. One of my friend said that DSLR footage should be imported in Avid through an AMA link setting so that other apps like FCP and colour correcting softwares could read them when imported.