From the information tagged to the ticket I see that you are the 2012.2.913 version, which is quite an old one. Through the years and Kendo UI releases, Kendo Window has been improved and fixes according to positioning, size and so one has been included. Thus, I suggest you re-testing the situations you are after with a more recent version.
On a side note, you can do that in a simple dojo (http://dojo.telerik.com/), which support recent versions of Kendo UI. Plus, this way you will be able to build up a sample and show what your is the difficulty you have with the Kendo UI widgets.
As for popover functionality, Kendo Window is a lot more than just a popover component and provides much more complexity in terms of functionality and UI. Therefore, it could be challenging to use it in such a basic situation. Have you considered using the Kendo Popup widget instead? It will enable you to create a very simple popup, position it easily and show it relative to whatever element you need to.
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