How can I solve false duplicate in Mail.app?
Sadly enough, I can't help you on why Apple's Mail think your mails are duplicates.

I have two ideas to fix the problem though.


Rebuild your Mailboxes (Select all your mailboxes, then in the Mailbox menu, choose rebuild). Wait the process to end completely (check nothing is being done in the Activity Window), then restart Mail;
If this does not work, you can always disable the option that groups mails that are related (In the preferences, in Viewing, de-select "Include related messages"). This is not ideal as it disable one of the main features of Lion's Mail, but if it's buggy…