I'm not sure if I've found a bug here or not. I can't really explain the behaviour I'm seeing, so am calling out for any help figuring this out...
I just installed the pixture_reloaded (and adaptivetheme) theme. I found that the search box wasn't in the list of available blocks (not in any of the installed locations, or the disabled list). It took me a long time to figure this out, but looking directly in the 'block' database table, it said this:
| 113 | search | form | pixture_reloaded | 1 | -10 | dashboard_sidebar | 0 | 0 | | | -1
..which basically says that the search block is in region "dashboard_sidebar", although the pixture_reloaded theme doesn't have a region with that name. It seems that if a completely valid block is in a region that the theme doesn't have, then that block just disappears.
(I resolved the problem by poking "header" into the region field for the row shown above).
I'm wondering how the blocks table gets populated? How can it be getting populated with duff info? Further, how does the blocks menu read it? Presumably it's not saying "if this table entry isn't in a known region, just call it 'disabled'", but does anyone know what's going on?