Am having the same problem with a client of mine.

Page that shows the sub-categories:
https://my1.bizshop.com.au/thepondsh...index&cPath=57

Page that doesn't:
https://my1.bizshop.com.au/thepondsh...index&cPath=25

Have checked the top categories and noticed no differences between the two, no orphan products in categories with sub-categories either.