Sagar - I had the same issue but was able to resolve it.
Like yours, my app started as an iPhone app which I "upgraded" to a Universal app using the XCode wizard. I noticed that when running on the actual iPad, starting in landscape, the app would start in Portrait, then maybe rotate to Landscape. On the simulator, starting in landscape, the app would start in Landscape, then the simulator would rotate to Portrait.
On the iPad, my app is a split-view app with TabBarControllers on left and right. Each tab is a view controller that returns YES to shouldAutoRotateToInterfaceOrientation.
I noticed that a brand-new wizard-generated, simple-case with a splitviewcontroller, Universal app didn't have this problem.
The difference I found between my app and the simple-case was that I wasn't adding my splitview-controller's view to the app window in applicationDidFinishLaunchingWithOptions. Instead I was showing a "loading" view at this stage, then later when an initialization thread completed I'd add my splitviewcontroller's view (and hide the "loading" view).
When I added my splitviewcontroller's view to the app window during the call to applicationDidFinishLaunchingWithOptions everything started working fine.
There must be some magic that happens on return from applicationDidFinishLaunchingWithOptions???
Is your app similar to mine in that it isn't adding the main view controller's view to the window during applicationDidFinishLaunchingWithOptions?