Cyan, you've hit the nail on the head.
If you'd use a good external converter, you would hear an immediate and dramatic improvement in sound quality. You will hear it on a single track, and its get to be a bigger and bigger difference once you start layering tracks. Playing a keyboard through a good converter will blow your mind.
Clock accuracy is a misunderstood thing in digital sound. Most people, even pro's, haven't quite got to grips with the fact that a clock effects the sound, and that a low quality clocks cause most of the synchronisation problems in digital audio. I think this is because its a synchronisation clock - and somehow people do not make the connection between that and audio.
To put it very simple, digital audio is a data stream, and the data has to be kept in the right place, all the time. When you're tacking, when you play-back. That is the clock's responsibility. Of case, this data stream is converted back to analogue audio for you to hear it, but if the clock does not do its job accurately, you can lose a bit here and a bit there, reducing the quality. Multiply that by 5, 10, 20 or more tracks........... and you'll get the picture.
In the post production world this has been understood for some time already, as they don't just have to sync sound, but sound to picture with sample accuracy. Add to that that some post houses have between 10 and 20 mixing rooms in one building, all working through one central machine room, where everything has to run to perfection. That is the reason why Studio Synchronisation Clocks currently on the market are expensive (between 1,5 and 2.000 - which is cheap considering their importance and the job they do). I think this will soon change, with clocks being developed for DAW's especially. This would solve multiple problems in one swoop for anyone using DAW's.
That's the simple description, if you like I could post a more technical one in the future.