You've not posted enough code to really see what you're doing, but one approach to the problem of dismissing and pushing view controllers clashing in this way is to make a the pop+posh into a single atomic operation operation, rather then seqential operations.
You can do this by using the setViewControllers:animated:
method on UINavigationController
. This allows you to effectively remove one or more view controllers, and add one or more view controllers, all as one cohesive operation, with one seamless animation.
Here's a simple example:
[self.navigationController pushViewController:loginController];
// ... later on, when user login is validated:
NSMutableArray *viewControllers =
[self.navigationController.viewControllers copy];
[viewControllers removeLastObject];
[viewControllers addObject:[[MyNewViewController alloc] init]];
[self.navigationController setViewControllers:viewControllers animated:YES];
If you do things this way, your code will be more predictable, and will work across iPhone and iPad.
For more info, see the API docs.
Update
Since your problem involves a modal dialog on top, try using setViewControllers:animated:NO
to change the nav controller stack underneath the modal login dialog before you dismiss the modal.