I am trying to make the opacity of body to 0 for some time and then make it to 1. But the problem is in IE after getting the opacity to 1, page is looking some how different.
The reason that it's rendered differently is because there is still a filter applied to the body. Although the filter has no visible effect due to it's settings, the rendering still has to support the filter as it's there.
You have to examine how the opacity is set, and make sure that the filter is removed once it's not needed any more.