Visual Studio 2008 should remember where your Find and Replace window was the last time you opened it, unless something was working on your system. I just checked the behavior on mine, although it seems to constantly appear where I last opened it.
So, try moving it and then closing and reopening it, is still displayed in the wrong place?
In addition, do you have a visual studio maximized on one monitor, or just stretched in a non-maximized state on both? Do you use any multi-monitor utilities that can change this behavior?
Alternatively, you can try the built-in search (Ctrl + I by default in VS2008) ... to search for a single file is generally better.
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