apt-get gives an error message, but that's all... then everything works just fine.
Apper gives the error message and then keeps complaining that the package cache was not refreshed.
As an aside: apper is really too picky about the package cache not being refreshed.
If I refresh the cache using apt-get, apper should realize that the cache was in fact refreshed. However to have apper see a cache refresh, you need to refresh the cache from apper. Why cannot it just look at cache files access times?