1) I agree with AndrewD, it looks like a tube sizing issue to me. Your tube is bigger than the rigid cane portion of your autosiphon, thus it cannot fill the tube completely, and air gets trapped. I'd be concerned about oxidizing your beer at this crucial phase. Try a smaller tube. It should fit perfectly - you shouldn't even need that metal hose clamp, it should fit snugly with simple friction.
2) You're right, you don't need to worry about disturbing the grain bed during batch sparging. Indeed, you WANT to "disturb" the grain bed. You should be pouring the water in, and stirring the heck out of it to extract any remaining sugars, before closing up your MT and waiting 10 minutes for it to settle down again.
When doughing-in, add the water to your MT first by just pouring it in directly from your HLT - no siphoning necessary. Then after your water has cooled to the desired temperature, sprinkle the grains into the water, stirring constantly to avoid dough-balls, then keep stirring until your temp has dropped to the desired mash temperature (it should already be almost dead-on if your calculations were correct). My autosiphon doesn't get dusted off until I rack from primary to secondary before cold-crashing and adding gelatin, then again 2 days later during kegging.