I contacted Motonation and I'm sending in my boots today for them to check for warrenty work. I wash my boots everytime I wash my bike if they are muddy, if not, I just leave them as they seem to take a long time to dry out. I didn't think about water proofing them, didn't think I should have to... there motocross boots... I kept them as clean and as dry as I could. To their credit, everything else held up great. The soles look good after a full season and all the buckles are fine. I didn't think I was hard on boots. I just ride, and most of it is on the track so its not like I'm kicking rocks or tree roots.
I should hear back from motonation in about a week so I'll keep it updated.