It could also be as simple as just restarting discovery server. I have found that over time discovery loses track of the complete list of hubs it needs to visit and will eventually reach a point where it only revisits a small portion of your total number of hubs.
You'll want to pull the latest version of discovery (that's compatible with your UIM version) off the hotfix page and use that.
A prophylactic restart of discovery weekly or more often will go a long way towards cleaning up discovery's weirdness.
Alternatively, make sure discovery isn't crashing part way through the list of hubs - it might not ever be getting to some of your hubs.
-Garin