Funnelback doesn't perform caching of queries - results for a given collection+query will only change as frequently as the contents of the collection.
Other items to check:
- If you've updated the Funnelback results template, have you published it via the Funnelback Admin UI?
- If you remove Matrix from the equation, and access the Funnelback Public UI directly, do the results appear as expected?
If you've checked both of these, I would suggest that the caching issues lie outside Funnelback. The Matrix REST asset should be investigated next.
Note: Funnelback defaults to retaining cached copies of individual, filtered results. These are also updated every collection update (if the source content has changed)