I am using LyX under Windows and OSX. For the same file (class: article) OSX-LyX generates \usepackage[T1]{fontenc} whereas Windows-LyX does not.
Result: LaTeX/TeX don't not do their job (plenty of error messages apparently related to unrecognised characters in the bibliography) for the Windows version whereas is works perfectly under OSX. (NB: Of course I successfully tried the obvious remedy: add \usepackage[T1]{fontenc} to the user-defined Windows-LyX preamble. But that leaves me wondering why Windows-LyX does not do it in the first place, just like OSX-LyX does it.)