Annoying pick struck noise when recoring thru line

I have this same exact problem and it drives me nuts. I use a 2mm pick also but that definately isn't the problem. I've tried different picks, different pick angles and picking one note as precisely as i can and it still makes the farking noise. I'm gonna try lowering my pickup as Dandelium suggested when I get home from work as I have tried everything else mentioned in this thread. :Spin:
 
i'm going to bet it's the pickups. try recording with a friend's guitar or something. a guitar with emg's could help.

you definitely need to use impulses though since you are recording direct, and not actually micing up a guitar cab! check out catharsis' thread for some very popular ones.