Right out the gate I going to say it's human error, whomever is taken the cap off is moving the frame some or the cap in some way or the other. If you think it's the machine try doing a flat sew out, stop it, remove the bobbin and replace with a new bobbin and backup same as you do your caps and see what happens, if the alignment is off then you've got a problem in your machine, if it sews out fine you got a problem with whomever is removing the the cap and frame. Make sure your caps are hooped good and not to loose so they don't move a little if you have to take them off during a thread or bobbin break.