The invoices may be batched over but not going where you expect.
So, please confirm the Company Directory matches: (see image)
Then confirm each installed integration instance split invoicing module (see image):
Then run maintenance error checking and reindex data files: (see image)
Sage UK have been known to have data corruption issues which is not something we can resolve if that's the case. But if these solutions don't work, please contact Sage support.