/any_mod/maps/start.bsp will find /id/maps/start.lit and load the sucker, if it doesn't have it's own .lit.  Not pretty. 
This can happen for any maps with duplicate names.  A lot of mods have custom start maps, so that's probably the most common.
Fix options:
1.  Check that the absolute paths of the .bsp and .lit match.   A bit of work, model_t only stores relative paths. 
2.  Compare .lit file size to lightdata (the standard lighting).  The .lit file size is lightdata * 3 + 8.  Doubles as an integrity check.
Similar 'add-on' files types like .ent may have the same issue.
			