Yes, that function’s conditions is:
return empty($permalink_structure)||strpos($permalink_structure, '?')!==false||strpos($permalink_structure, 'index.php')!==false;
Clearly it’s the last part that’s always returning true, because all of the predefined WordPress URL styles contain index.php (except for one, which is the query with ‘?’).
Doesn’t this appear to be a bug in qTranslate-X?
Anyway, I tried a custom URL style which doesn’t include index.php, and surely enough it didn’t work; the pages no longer load (404).
Thanks for your help