I realize it's a colossal pain in the butt to climb towers to test antennas, but I would take signal readings across a band, then build a vertical dipole or ground plane antenna for that band, install it in the same spot as the Scantenna with the same LMR-400, and see how it compares. If it's _worse_ than a dipole or ground plane, you have problems.
My guess is that you may be seeing front end desense from having such a _good_ antenna, picking up a nearby signal. I'd search for all signals in a 1 or 2 mile radius from your location.
1: visit
http://world.maporama.com/idl/maporama/drawaddress.aspx, type in your address and find your coordinates at the bottom of the map
2: visit
http://svartifoss2.fcc.gov/reports7/lat_long.cfm?accessible=NO, select "Point Radius" and try first a 1km, then a 1mi, then a 2mi search.
This will take you some time but power levels are listed on each licensee's page, if you find a pager or digital site that's spitting out a few hundred watts near you that could overload your radio and desensitize it across the board. To test suspect frequencies, program them in and see if you can receive them inside the house with no antenna, or if they come in full-scale with a paper clip in the BNC jack or something ridiculous like that.