Was this on an '05? I hadn't heard of any issues with the later bikes.
However, when I first got my '05, I thought I was having a problem -- every time I pulled the filter to clean it, I felt bits of dirt in the boot. Turns out, the dirt was falling off the filter into the boot as I removed the filter, not going past the filter while the bike was running. I started putting a small plastic grocery bag over the filter before removing -- end of problem. Since then, I've not had a speck of dirt in the boot.