The question is, how did it get off factory settings?  With the EZ Command all you can really change is the locomotive address and the direction of travel.  My guess is there is some other issue probably with the way you are programming the address.  Read the instructions on this again.

If you're using the Woodland Scenics System the homosote is unnecessary and if where you live is anything like where I live you won't be able to find it anyway.  Just use cork or foam roadbed (Woodland Scenics) on the foam risers, glue the track to the roadbed using caulk as recommened, and hold it until it dries with the pins sold by Woodland Scenics.  When its dry, ballast the track it the traditional way, alcohol or wet water followed by a soaking of white glue (the good kind not what it sold for use in schools) mixed 50/50 with water.  When it dries the ballast will have more that enough strength to hold the track even if the caulk fails which, if you did it right, won't, fail that is.

Try taking the spring out of the pilot.  I had a similar problem with the pilot de-railing on my Bachmann Ten Wheeler.  After I finally  removed the spring I have had no problems with it.

Ray