I too had "recumbent knees" when I began riding bent. The things alreeady mentioned worked for me.

Shorter cranks, I went to 155s
more spin,
stretching before riding ,
seat closer to pedals than intuitive set up. (I wound up with a bit of flex in my knee being best for me)

Also, I developed the habit of down shifting at every stop. The leg press nature of bent start up made that a big help for me.

Hope that helps
Tom