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1. Cancel the "downloading" bar at the top when Cydia first opens, to prevent the "reloading data" alert from popping up
2. Go to manage > Sources
3. Remove all sources except for the default one, BigBoss (should be http://apt.thebigboss.org/repofiles/cydia/)
4. Reload Cydia and let the "downloading" bar complete its cycle. Let "reloading data" pop up and see if it works normally.
5. if this fixes the problem, add back all sources you were using one by one, reloading after adding each one, to track down the problem source.
If this doesn't work, you could always reinstall cydia by re-applying the jailbreak.
NEVER RESTORE IPHONE cause it will force you to update your iphone and its hard to find latest jailbreaks for that.