Just checked mine, everything seems in order except for iMobileCinema, which has been giving errors for weeks. If you just rejailbroke, though, Cydia might be trying to download different indexes or something.
I was downloading something and was almost finished as "Reloading Data" comes up as usual after a download, then that message came up. It shows now that I don't have any sources, packages, nothing. I've restarted but that didn't work. I hope it's just a server issue.
I got fed up with Cydia being so flaky, restored my phone as new, and I'll be living without a JB. Just not worth the hassle and instability IMHO. I will miss Lockinfo and QuickReply SMS, but hopefully these features show up in the 4.0 update.