How about trying some simple things to figure out what's wrong. Reboot the PC to start from scratch. Load just one copy of WoW. Don't rename it. Load this new file. Press F2, F3, F4, F5. Each time it will try to move that single WoW to one of the four spots. I'm leaving renaming out completely in case that's the problem.

Code:
<Hotkey F2>
<TargetWindow "World of Warcraft">
<SetWinSize 512 384
<SetWinPos 0 0>

<Hotkey F3>
<TargetWindow "World of Warcraft">
<SetWinSize 512 384
<SetWinPos 512 0>

<Hotkey F4>
<TargetWindow "World of Warcraft">
<SetWinSize 512 384
<SetWinPos 0 384>

<Hotkey F5>
<TargetWindow "World of Warcraft">
<SetWinSize 512 384
<SetWinPos 512 384>