mmh82 As per initial thought, The Search Engine Friendly (SEF) URLs arent configured properly due to which site links arent appearing right as envisaged.
For review purposes :
1) You may try assigning default Joomla template - protostar and similar results will appear
2) Turn of SEF urls in System > Global configuration > Seo settings
and the links will start working right
Solution :
Kindly follow the documentation in order to ensure SEF urls are configured properly - You may also follow this tutorial which defines almost similar instructions
Also, To append, Please follow documentation for JA Focus as suggested by Pavit in order to configure respective menu items