This could lead to a problem if the user's screen resolution is low and in consequence the upper and lower part of the dialog is always out of the viewport. Imagine a dialog where the submit button is at the bottom of the dialog page:
In this case it could be possible that certain users never see the button and therefore never could submit the dialog.
A solution would be to deactivate the repositioning if the scrollbar of the main window is used. Unfortunately, Dojo's Dialog has no configuration option for this.
Digging in the source of Dojo I end up with disabling the event that is fired on usage of the scrollbar. Tested with Dojo Version 1.4: