I have the same problem.
It happens when I run Update manager in the following scenario:
I run update manager 
then I click check
after repositories are downloaded the error is shown
After the error the list of updates is refreshed and it looks to me like every 
thing works fine after.
If there are no updates the error doesn't show. 

BTW I'm using ubuntu 9.04 Beta, it happens on Alpha 6 and most probably
5 as well.

All the Best
Lulzim

-- 
E: The package cache file is corrupted E: _cache->open() failed, please report.
https://bugs.launchpad.net/bugs/257639
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