What ArcMap version was the .lyr file created with? Generally, the .lyr files are version-sensitive and not backwards compatible.
Other than that, I'm not sure why it wouldn't work... It's not a composite layer (made up from more than one GIS layer), right?
You could just recreate anew it your script (MakeFeatureLayer, AddJoin)... That's what I do (rather than using a .lyr as the data source).