Hi grasshopper.
Assume that you've checked the teeth / gearing on that section of the rail that is aligned / meshed with the drive cog when the window is fully down.
Haven't had the problem with either of my Disco's, but have experienced similar in Ford F100 a while back. Problem there was loose linkages on the main (driven) rail which pushes the window up & down. During most of the range of movement, the rail remained fully engaged with the drive cog, but when window was fully down, there was enough movement in the linkages holding this rail in position that the rail was able to move slightly away from the drive cog, allowing the gearing to slip. To fix, I drilled out the linkage holes to a slightly larger diameter than original (so that both holes were exactly the same size, and replaced the original linkage pin with a bolt of the same diameter as the holes. Then used washers and two nuts locked together so that linkage was loose enough to allow movement, but nuts would not come loose. All worked fine after this fix.
Don't know if this will be the same problem / fix in the Disco, but it's where I would start looking.