Does your exported wave have these same qualities? That's what you want to check first. I believe soundcloud will re-encode your mp3 and what you may be hearing is the re-encoding artifact as it will be at a lesser quality.
Any time you are having this issue, export your audio out of Sonar via wave file first and listen to it that way. If the wave is ok, go back into Sonar and export an mp3 and check it. You will pick up warbling effects from mp3's created at 160 kb and below. From 192 kb on up, you shouldn't hear any artifacts. If soundcloud is re-encoding to lesser quality, that's the problem and it's not on your end.
-Danny