Haven't come across this problem before but you can try this :-
In windows explorer, go to C:\Documents and Settings\[your user name]\local
settings\microsoft\windows Live Mail
In there you should see a bunch of folders (hotmail etc., one folder for
each mail account you have setup).
Within these folders you should find folders marked inbox, sent items etc.
Take a backup of these folders (just in case) then go into each folder,
inbox, Junk e-mail, Sent items, drafts and deleted items and clear out any
files in there.
Do this for all your mail accounts.
Once that's done, load Windows Live Mail and try re-syncing your accounts.