Mano, it is my understanding that Browsers get the fonts they use from the 'local machine', not the Server. If the custom font isn't installed on the local machine, the browser will substitute the closest related font. I just completed a project using custom fonts. Before we began, we made sure that everyone wanting to browse to that viz downloaded and installed the custom font.
I really don't think putting it on the Server had any impact on the font that was displayed. I also don't believe that the custom font displayed correctly without being installed on your local machine. I suspect that the font difference between IE and Chrome was a matter of which font the two different browsers chose to substitute in. I don't know how you had things setup so I could be wrong on this.
Here's a good resource: How Browsers Manage Fonts | Practical Ecommerce
Did you ever figure this out? I'm having the same issue.