Are you using compiz or metacity for window management? There is a different solution in each case.

For compiz (or "Visual Effects"):

• First you need to install the compizconfig-settings-manager package, if you haven't done so already. (I'd put in an apturl link, but this board seems not to parse them correctly.)


• Then open System -> Preferences -> Advanced Desktop Effects Settings and choose the "Window Rules" plugin.


• In the "Above" field, add the following:
  title=^Document Preferences$ | title=^Add/Edit Citation$


• Lastly, go to "General Options," the "Focus & Raise Behavior" tab, and set "Focus Prevention Level" to Off.

(For more information about window rules in Compiz, see: http://wiki.compiz-fusion.org/WindowMatching)

For metacity, you should be able to use the application called "devilspie" to set up rules for the plugin windows. I used to use this method, but when I just tried my old rules, they didn't work for some reason. So, rather than posting apparently broken rules here, I'll post a link to a wiki that explains how devilspie works instead: http://foosel.org/linux/devilspie

I've always needed to use some extra window management like this to get the plugin windows to appear and stay on top of the OOo window. I don't know if that's some kind of linux-only quirk, though.

Thanks for the feedback.

I've added a section on window management rules to the Zotero page of the Ubuntu community help wiki, which has some additional tips for Ubuntu (and other Linux distro) users. Please feel free to fix any errors you may find there or to add any other information!