Hi Simon,
First of all take a look, if you have acces into the database, the table t_category_stats because is where the counters get the data.
In addition, this stats save for each subcategory, so if you insert items (for example) in "animal" and it's a subcategory of "for sale", in the root category the stats will show 0 items. Is this your problem?
This is something we're working on.