Sounds like me, up to just recently. I switched to 'bents last fall, and was having a lot of knee issues until early this spring, when everything just seemed to straighten itself out. In retrospect, it just took my knees that long to adapt to the different demands put on them by 'bent pedaling. Just make sure you're not over-extending or over-flexing your knees. The range of motion should be similar to, or less than your df range, and a lot of folks swear by short (like 150mm) cranks. I went from 175s on my df to 170s on my bents and that seems to be working well. So, the short answer is, make sure your leg extension is correct, and your crank arms aren't too long, and be patient. Oh, and Icy Hot and ibuprofen help...