When you clear cache ad counts per category is cleared.
How many categories and locations you have? ad counting is automatically disabled if you have categories x locations > than 500,000.
Also make sure that you are viewing all locations and all categories. Because if you are in other location than current ad is then you cannot see it in count. For example if ad in London, and you are viewing ads for Bristol then that 1 ad count will not be shown because London and Bristol are in same level. Yo can view ads for all locations by clicking Home link or pasting /home/ after your sites’ URL (exaple.com/home/)