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I had the same problem today on my site. Is there a bug going around? I'm using 2.0.12a. I haven't yet taken the time to update/upgrade to 2.0.13.1, but maybe I need to? Is this an exploit?
My theme was showing just fine, but no block content was showing AT ALL!!! The module pages would work and display, but no blocks were showing. When I went to the System | Groups page and went to check the various permissions, that was all correct. And, when I clicked on a particular block it seemed to be set alright. But, again, none were working.
Anyhoos, what I did to fix it. I tried updating each module per an old posting, but that didn't seem to deal with it. Then I went to the System | Groups page and clicked on the Webmasters group and submitted that. Then I could see them again in the System | Blocks area (after choosing to see those not visible).
Now for some reason or another, they are all working again. Don't ask me what is going on, but I was sorely confused about it all.
Over the past few days, I'd been starting to add caching to my site, but I can't believe that contributes to this. Hope this helps some of you.
Befuddled and almost bemused....