Interesting. i guess it could be a WM "feature". Metacity is surely weird enough; but as I said, OOo is the only app that I have any trouble with. Gimp opens a hundred windows, but it never does this:
Here's another one that's a lot of fun. In Calc, I bring up the function wizard to work on a formula. I click the "Help" button on the function wizard. The Help window opens, on top of the function wizard as it should. Now, leave help open, bring the document & wizard back to the top and click "Help" again. Now help pops up, and immediately goes away,
under the Calc document window. I wish I could make a video, it's hilarious (unless you're trying to work). I have two text documents and a spreadsheet open, and the windows fly up, down and around like a house of cards in a hurricane.
Both the Fedora OOo build and the OO.org build do exactly the same thing, so I assume it's something in the OOo code that causes it--or at least something that interacts badly with the WM. And I just tried it under KDE: same thing. So it's not just Gnome/Metacity.