Ok so I thought about it for awhile. When I have used amp sims and stuff in the past I have noticed an issue with the high end of the frequency spectrum not being where it should be. (Missing) I thought this was an issue with my guitar. Well I actually just got a new one. High end issues were the reason I actual bought the new guitar in the first place. So I checked it out with a spectrum analyzer. Then compared it to my old one and they are the same pretty much. I then took and compared it to someone else's DI wav and analyzed it as well. Here is a pic of what I found.
The two on the left are mine. One is direct into interface and the other through the Axe. Finally the one on the right is someone else's. There is a steep drop off from about 1500 on-wards on my two in comparison. I'm not sure what could be causing this. Any ideas? These are DI guitars btw.