HI Phani,
As you mentioned that you dynamically create a <iframe> element to load some page, is the page (loaded in iframe) of an external website (rather than some pages in your Windows Store app project), correct?
When programing Windows Store app with HTML5 and JS, we might need to take care of something which might be somewhat different comparing to standard web page based web applications. The HTML DOM and supported APIs is different and there exists different
context for loading local and external web pages(for security restriction purpose). Here is the msdn reference talking about this:
#HTML, CSS, and JavaScript features and differences (Windows Store apps) (Windows)
http://msdn.microsoft.com/en-us/library/windows/apps/hh465380.aspx
Also, the following book is very good for Windows Store app developers using HTML and JS.
#Free ebook: Programming Windows 8 Apps with HTML, CSS, and JavaScript (First Preview)
http://blogs.msdn.com/b/microsoft_press/archive/2012/06/04/free-ebook-programming-windows-8-apps-with-html-css-and-javascript-first-preview.aspx?Loc=zatfz_zTS1z&media=zBKz&tech=zSdz&prog=zPressz&prod=zWin8z
For your case, if the pages you want to load in iframe is not from an external web site (but some static html content pages in your local project), then you can consider using those built-in single navigation approach to load the html content (without completely
reload the entire page framework or using iframe).
#Supporting navigation (Windows Store apps using JavaScript and HTML) (Windows)
http://msdn.microsoft.com/en-us/library/windows/apps/hh452761.aspx
And this is also those built-in project templates (such as the "Navigation App", "Grid App" or "Split App" uses).
If the page does be an external web page or you must use iframe to load it at runtime, then it does be possible that the frame windows will blink when the iframe start loading page (since it will need some time for it to load the entire pae and referenced
resources before rendering the UI). That's also what we might see when loading a page in standard web browser. Just like when we embed a webbrowser control in WPF or windows phone application, to avoid the blink or white screen at loading time, we can consider
using some UI animation such as displaying a div over the iframe or hide it first and show it after a while.
Please remember to mark the replies as answers if they help and unmark them if they provide no help.