Ok so you are Exporting your song from Sonar once you are satisfied with the mix as a 44.1/16 Wave file.
You listen to this mix using the same system and a player ( software) that does not have any sound enhancements enabled ( common issue)
You even tried importing the wave file back into Sonar to test too.
You are listening using your audio interface ( Alesis ) and not any On Board sound cards ( which should be disabled anyway)
You are still happy with the mix and you burn this wave file to a CD using Nero or a any CD burning software.
And it sounds different when played through the same system?