Thanks for posting.
Is this an ESD (Electronic Software Download from FileMaker)? Try removing the current download and download from another browser.
Also, what is the service pack version of the W2k3 machine?
Even though it is a new machine, try booting into Run > MSCONFIG > Services > hide all MS services checkbox > Disable All button > Apply and reboot. Then try running the installer.
Let me know how it works out
Bingo... FMS need SP2. THANKS!