I would guess (I'm no expert though, by ANY means) that while standing, you might either be dropping your bow arm at the shot, or are starting the shot with your bow arm at an angle lower than 90 degrees from your spine. While shooting from one knee, you subconsciously are keeping your bow arm up for fear of making contact with the ground with your lower limb.
OR, it's just that the target is closer to your shoulder height while kneeling. Remembering to consciously keep your bow arm 90 degrees from your spine and to bend at the WAIST to shoot at a lower target might help.
Just a thought....hope it helps.