Without running the numbers, my personal rule of thumb is that when dispersion jumps counter-intuitively beyond a specific distance, there's probably some sort of transonic effect at work. Another rule of thumb is that for a reliably stable POI out at the near-transonic region, it's best to load for a minimum of 1300fps at the target's distance.
Shooting at Sea Level makes all the Sonic/Subsonic issues just about as critical as they can get, unless one shoots at the Dead Sea level or out in Death Valley.
Finally, BC is not a constant value, but is dependent on actual velocity. As velocity drops, so does BC, usually (some shapes more than others); so bullets shed velocity faster and faster the slower they get (I.e.
BC data for 142SMK). My own experience is also that as the trajectory angle gets steeper, effective BC drops even more due to pitch/yaw angle. The faster the twist, the more pronounced this effect becomes.
Whether or not these issues are at the root cause of your questions, retained velocities are adversely affected as altitudes drop. When I first shot my 260 at 1000yd, it was at roughly 6000ft ASL, and going over 1100yd was not an issue. I have never shot LR at Sea Level, but questions like yours don't surprise me very much. I would think that sonic transition velocities could be susceptible to influences as small as temperature and barometric changes at such low altitudes.
Greg