I am attempting to use the Extract LAS tool to create a subset las dataset to test workflows to get a better DTM output, as suggested in this article. I created a 2D polygon that outlines my target area and have run the Extract LAS tool several times trying different settings and I keep getting an output dataset that is missing regions of points within the extracted area. I can't tell if the points are actually missing or if they are just not displaying, but either way I can't get most or all of the points in these regions to show up, no matter what I do. I have changed the symbology, cleared the cache, zoomed and panned around, refreshed the display, removed and re-loaded the dataset, re-calculated statistics, and more with no success. Here is a screenshot of what it looks like: 
When using the Extract LAS tool, I have used my polygon in the Processing Extent portion, Extraction Boundary portion, and both simultaneously. I have ran it with "Process entire LAS files that intersect extent" checked and unchecked, and tried a few other combinations with no success.