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.)