To disable automatic grouping of duplicate messages, quit Mail then run this command in Terminal:
defaults write com.apple.mail AlwaysShowDuplicates -bool true
To revert to the default setting, run this command:
defaults write com.apple.mail AlwaysShowDuplicates -bool false
or simply delete the setting altogether with this command:
defaults delete com.apple.mail AlwaysShowDuplicates
If you want to see how Mail behaves with this setting enabled, but without modifying your preference file, start Mail from Terminal with this command:
/Applications/Mail.app/Contents/MacOS/Mail -AlwaysShowDuplicates YES