Yesterday I tried some changes to the background colors in my site www.fotocomefare.com. I then reverted all the changes.
In Firefox and Chrome site's appearance is correct, while in IE the container background color is sort of overridden by the body background color.
Before the changes (which I reverted) it worked also on IE.
What's the matter?

What were the changes?
Where did you make them?

I changed background: #ddd in the Style & Configure Layout page.
Then, I enclosed the custom header I'm using in a <div style="background:white;"> tag, in Style and edit header area page.
I added background:white; in Style and edit CENTER COLUMN page, Center column style box.
Finally I added background:white; to the Style WIDGETS page, Widget container box.
Then I set Layout backgroung back to #fff and it worked in every browser except IE.

looks the same to me. I do notice that you have a caching plugin active. This can cause the delay of seeing a change you make. you should always turn them off and flush the cache when making changes.

Thank you, but I already flushed the plugin.
Can't there be another cause to the problem?

Like I said when I look in ie8 I don't see a problem.
What version of is?
Can you post a screen print?

I attached 2 files a Crop of the top right corner of the page in Chrome and in IE 9.
You can see that the padding in IE has a wrong color.
While inspecting the page in IE 9, I found out what the problem is. When the page is loaded, document mode is set to IE7 standards.
I disabled the Emulate IE7 options I recently enabled, to try it. However the behavior doesn't change.

did you set ATO->Style & configure LAYOUT->IE Document Type to 'IE9'

looking at the images side by side, it looks like IE9 is adding some extra padding at top and has moved the logo up some. Notice the gap between the logo and the next line 'La fotografia digital...' is bigger in IE9

In IE8 there is no gray at the top of the page. Don't you just love the way all browsers work the same - even between releases (NOT!)

I can't see any IE document type in my style and configure LAYOUT page.
Probably it's because I still have Atahualpa 3.6.4.
I'll try and update.