my cyan had the "open position" issue for the past month. I don't think it was a gear "engaging" issue, because the yellow (which is operated by the same gear) was holding fluid just fine.
Naw, didn't mean that the gear wasn't engaged, just that you could advance the gear to lock the pump. As Artbot said, there's a position in the pump that pinches the lines. It's possible that one colour could be pinched, and not the other, either due to misalignment in repair of the pump, or broken gates inside the pump mechanism. Manually advancing the gear is a way of forcing the internal rollers into getting moved by the gates, thereby pinching the line.
If that still doesn't keep fluid in place though, those gates are probably busted. Like I said, either repair or replace, depending on one's level of comfort.
@Artbot - I kind of like the idea of the pump locking. If it's open all the time, then technically the heads resting on the caps are exposed to air (unless the waste solvent is above the point where the lines enter the waste bottle, of course). With the lines pinched, you have an air-tight environment. If I feel the need to flush fluid down the caps without waiting for Disway, I just advance the pumps until all the caps are in the open position.
Edit: On a sidenote, I love that mod. Saw it in a previous post of yours, and put it on my to-do list.