Different sofware definately sounds different and its not about noise at all. All software has to use some form of algorythm to handle all that audio and different algorythms achieve different results. For example the latest version of Logic actually sounds alot different to the version before it. Cubase does have a somewhat cold sound to it, Acid has a warm mushy sound to it.
I hate cubase more the more I use it. I think I'm gonna try Sonar next. Don't really like logic, its not logical to me anyway even though its probably the best sounding sofware out there.
Can't get cubase sx 1 to work properly with midi. I try to do the same thing in Acid and it works straight away. But acid is an unstable piece of crap and it puts way too much strain on the pc. I can have 3 times the amount of tracks going in cubase and the pc is sweet as. Cubase is just a complete piece of crap to edit audio in.
Just having a rant anyway
but its very true that different software sounds different. And remember, if it sounds better, it is better!!!