As this has been bugging you for two months and sounds troublesome off the bike, why not see the doctor and stay off the bike for a bit before spending lots of money on pedals and shoes?
What angle are your knees at when clipped in? What angle are they at when sat on a table with feet dangling? Are they the same? Try flat pedals / pedals with toe clips and see if that helps? But I'd still favour staying off the bike and seeing the quack