The version of metacity that shipped with Fedora Core 5 includes the 'experimental strict-focus-approximation' feature. This is supposed to prevent applications started from a terminal window from stealing focus from the terminal. It has the unfortunate side effect that such applications appear underneath the terminal. Many users don't like this behaviour and until metacity 2.14.3 it wasn't configurable.
Versions of metacity since 2.14.3 include a patch to make strict-focus-approximation mode configurable and off by default. Updates for Fedora Core 5 with version numbers greater than 2.14.2-1.fc5.2 also include the patch.
For a while I maintained RPMs for FC5 that included the focus-new-windows patch. These are no longer required: you should use the official FC5 updates instead.
I do still maintain RPMs with my patch to implement manual placement of new windows. These are available from my Manual placement for metacity page.