Currently Being ModeratedOct 28, 2012 3:37 PM (in response to The Wine Bug)
This was too weird to be real. Apple mail does not show messages it believes to be duplicates, and buy, does it make big mistakes in deciding what are duplicate messages and what not! Some of my mailboxes had over 100 "duplicates" not showing according to apple mail.
I found a solution thanks to this topic:
defaults delete com.apple.mail AlwaysShowDuplicates
does yield an error in 10.8.2 ( Domain (com.apple.mail) not found. Defaults have not been changed. )
defaults write com.apple.mail AlwaysShowDuplicates -bool true
Does work brilliantly though!