Ok, what you can do:
 - close bitcoin
 - rename your old wallet.dat
 - run the last version of pywallet (must say 'Pywallet Web Interface v2.0b8-bt' at the top of the web page)
 - go to pywallet's "Dump your keys"
 - put "secret,label" in "Data to print" (see pywallet.tk to know how to fill the other fields)
 - hit "Dump keys"
 - open (with notepad) the file you put in "Output file" to check that all your private keys are there (if there's a problem you'll see lots of "#ERROR#" or something like that, in that case check the wallet path)
 - then run bitcoin again, it will create a new wallet as you renamed the old one
 - close it when it is launched
 - go to pywallet's "Import keys"
 - put the new wallet path (file=wallet.dat, directory should be default)
 - put the file containing the private keys in "CSV file path"
 - hit "Import keys"
 - wait a bit
 - open bitcoin and enjoy your cleaned wallet