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)