Probelm with Animation

Been having problem doing a motion animation. When i get my machine sequence all worked out, and save it, it throws some of the sequnces out of order and lose mates and unsupress mates at certain points that gives me a mess of an animation. Have attached my assembly,and you'll see some door,cylinder and lift out of sequence.

Does anyone have any suggestions on what to do?

Thanks

SolidworksMotion Studies