I'm running 10.6.4 as well, why not just switch over to Bootcamp? Or use VMware and virtualize Windows.
Now I'm 100% sure if this will work, because I don't have root and haven't done this myself. But you could probably navigate to /System/media/bootanimation.zip/android and manually edit all the wvga_htc_bootup_android images to the image that you want.
The only issue is that there's 78 of them, so that's a lot of manual editing.:/
Here's the Windows editor at
XDA.