I have an 06. it does seem to stutter sometimes when its still cold. this is the first i have heard of a possible difference so i will be listening quite closely. most of my stuttering went away when i change my inlet tube. and that could have been because of the jimmy rigged job a mechanic did to it just after i got it. he broke the boost controller nipple and replaced it with a wd-40 straw. yeah i know wtf!
Most of the minor problems that the '06 had were taken care of for the '07 model, and a TSB was released for all '06 models to fix it as well. I wouldn't say there's more problems with one year over another, it's just a matter of perception.