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Dan, the Garmin Swim can occasionally miss lengths for some users.
Make sure you do a strong push off the wall and a long glide phase so that the watch detects your movements. It may also help to wear the watch on the arm that does not take the first stroke after you turn.
The watch works by monitoring how your arms/body move using accelerometers. When you swim laps, Your arms moves in a regular pattern with each stroke. When you get to the wall, your arms stop moving, you make a turn (open or flip doesn't matter) and you push the wall in the opposite direction. This change in pattern is how the watch detects when you complete a lap.