Wallet appears to have the same issue the Hansa wallet had; in that if "Minimize to tray" is enabled but "Minimize on close" is not, it acts as if *both* are enabled.
I think that is what it is supposed to do.
I used that option now on darkcoin wallet, blackcoin wallet, and 2 others. All do the same thing.
It doesn't appear to be a bug, it appears to be doing what its supposed to.