It was a bit more difficult than I would assume, but there is at least one way of doing it;
Use the window functions of the LabVIEW Windows Utilities:
http://sine.ni.com/apps/we/niepd_web_display.DISPLAY_EPD4?p_guid=B45EACE3EF4556A4E034080020E74861&p_node=DZ53008&p_submitted=N&p_rank=&p_answer=&p_source=External
Now to get the behaviour you want you need to run the restore window vi, then the always on top window..(set it to activate the window as well).and then the revoke always on top vi...the application will still blink on the task bar, but the window will be restored, put on top and activated.
Mads