When I updated my blog to Blogengine 1.4.0.4 I kept my theme as is, since the blogengine new version is backward compatible. But there was an issue which is the Ajax loading gif will be visible by default below the comment box. I was planing to fix it this weekend. But fortunately Derek  pointed the issue, and which saved a lot of time for me (telling the truth at least two hours).

The issue was just a missing of a style in the CSS file. If you have the issue check whether you have the following class in your CSS

#commentPreview{
    display:none;
    clear:both;
    min-height: 150px;
}

This fixed the issue.

Once again thanks to Derek, who saved my time