Both my current boys are agility dogs, and have had a realllly hard time getting up from a 'lie down' unless given the 'break' command.
We've broken the older dog on this habit, as he's more keen, but I have stopped herding with my younger all together. He's my world team hopeful and I truly didn't want to muddle any criteria.
Honestly, I have no advice. Just wanted to let the OP know that we are in the same boat.