I had something similar last night...was trying to scan out some asteroids (yeah, worthless, but that "unexplored" on the system list just annoys me sometimes) and nearly ended up in the asteroid belt a few times, but the scanner never triggered. And yeah, my scanner was on, it just wasn't triggering for some reason.
I have encountered an issue scanning asteroid clusters (completist!), although not recently.
This mostly occured in belts around remote companion stars. I found that they _could_ be scanned, but the "sweet-spot" where the scanner triggers was offset from where the lenticular indicated the cluster should be. The offset was in 3D - so flying around would sometimes appear to cure the issue if the offset and lenticular happened to end up in the same direction.
Interesting comment about the planet being in a high velocity orbit... That could also be the case for near-star asteriods where this issue manifested for me.