I think your problem is coming from the fact that FOF is using an additional Installer class for database and schemas:
FOF comes with the FOF30\Database\Installer class. Unlike Joomla!, it doesn't base its actions on unreliable version numbers. Instead, it will run SQL commands based on whether tables / fields exist, the reported type of fields or the result of custom SQL copublic function updateSchema()
Thus it is suggested to place (call) two additional functions - for example - in your installer script:
public function updateSchema()
And at uninstall:
public function removeSchema()
And you have to provide a schema XML file with your component:
The schema files are provided in XML format. You only need one XML file per database technology. By default these files are stored in the back-end of your component, under the sql/xml directory. This is something you can override through the $directory parameter you pass to the class constructor.
And the full description of the reasons and use of the above is here:
You can see the usage of the above in one of the components from the author of FOF here:
I hope this gives some light on the subject for you.