A lot of times when I'm picking a lead a note might end on a down beat[down stroke] though the lead continues but with a down beat rest (quarter note rest) following the last note I played.I mistakenly leave my right hand at the down position through the rest and pick the next note (which is a down beat) with an up stroke. I think this problem exists with only me. It seems everyone else doesn't have this problem. I'm learning to keep my right hand moving continuously up and down so, only then will I hit the down beats with a down stroke.
Yeah, i've seen mentioned before when strumming rhythm, you can use ghost strums on the rest period, that way your strumming hand stays in motion to the particular pattern you are playing with. It takes alot of practice to develope.