When you activate SP on individual sites on a MULTISITE, the locations for SP resources (as seen under FORUM->INTEGRATION->LOCATIONS) are incorrect.
The workaround is to manually update the locations in the FORUM->INTEGRATION screens.
The correct option is to make sure that each individual site has their own default locations on initial activation - even the workaround will force all sites to use the same folders unless the admin has the skills to use sFTP / SSH to create new locations for individual sites.