A common workflow in Navisworks is to use 'Find Items' to make 'Search Sets' of similar items. Often, people will use 'Hide Unselected' to confirm that 'Find Items' worked. Problem is, the 'Clash Detective' will only find clashes in visible objects. To fix this, make sure that you toggle the 'Hide Unselected' button so that the entire model is showing before running 'Clash Detective'.
Autodesk should modernize the 'Find Items' tool to be more 'Google-Like' as well as more visual.