Upon investigating this a bit further, it seems the issue has to do with
the sort column and in particular the "package in main"/supported/logo
column. When sorting with this column, synaptic behaves excruciatingly
slow. Use any other column to sort and it's back to normal.

Eric M. Smith: Please try this and see if it helps, thanks.

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https://bugs.launchpad.net/bugs/658924

Title:
  Synaptic hangs several minutes (de)selecting or listing packages

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