This was an annoying little problem I had on 8.10 and bless my soul if it didn't occur on my fresh clean install of 9.04, so I thought I should throw the solution up here in case I need it again, or anyone else does.
Open a terminal and issue the following command
sudo update-apt-xapian-index
It will just take a couple of minutes to rebuild the apt database, then Synaptic should work fine again.
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