I sent an email to the WisconsinView manager and this was his response:
Jerry, the reason we have two sets in some counties is that a strict definition of Wisconsin County Coordinate System (WISCRS) parameters by USGS in the LAS header does not show up or visualize correctly in a map space used in ESRI products like ArcMAP. Its shows up shifted several miles to the SE in relation to other base map features. The folder labeled LAS_ESRI has the WISCRS projection parameters used by ESRI loaded in the LAS header. So if you are planning to use the LAS files in ESRI products I would recommend downloading the LAS_ESRI tiles. The USGS funded acquisition of many of the more recent counties in Wisconsin, so we offer those too.
If you end up with Wisconsin LAS tiles that appear to be shifted relative to other features in ESRI products, one can easily fix the shift by use of a .PRJ with the ESRI parameters for that Wisconsin county (hint: use the PRJ from the tile index shapefile and create .PRJs for all the LAS tiles - there's a script for that in the Arctoolbox). Likewise, in a LASD mosaic you can go to the horizontal coordinate system tab and fix the whole mosaic without changing the individual LAS tiles.
Its not clear to us who is right and who is wrong, or why the shift occurs at all. But with two big organizations who both know more than I do, its hard to get this fixed. In later collections, we offer only the USGS LAS tiles, but include a folder with the .PRJs too. Sorry for the confusion. I blame human stubbornness.
let me know if you need further assistance.
Jim Giglierano
WDOA