arjunblj,

Yes, Twenty Eleven gives Side Matter trouble. The problem is caused by a single rule in the theme stylesheet (line 721). To fix it, add the following CSS to your site:

.hentry {
    position: static;
}

If you set your note offset back to 0, notes should now be properly aligned. Unfortunately, this change will also make the comments link balloon next to post titles appear clipped and in the wrong spot. You can hide the balloon with the following rule:

.entry-header .comments-link a {
    display: none;
}