The game will run but I get a black screen from the start. When I open the game I can hear audio and the effects of navigating the menu. I'm using Windows XP Professional, Voodoo5 5500 PCI and am using the Amigamerlin 3.1 R6 drivers.

http://www.konami.jp/gs/game/mgs2_sub/english/index.html

The minimum system requirements are,
Windows 98/Me/2000/XP,
800 Mhz Pentium III or Athlon,
128 MB RAM,
3,8 GB free HDD space,
DVD-ROM drive,
Direct X 8.1-compatible graphics card with one of the following chipsets:
GeForce 256/GeForce 2/GeForce 2MX/GeForce 3/GeForce 3 Ti/GeForce 4MX/GeForce 4 Ti,
Direct X 8.1-compatible soundcard and Direct X 8.1.

try the latest SFFT A28.here:
http://www.3dfxzone.it/monitor/am/go.asp?url=88

Try running in Single chip mode, and see if you get the graphics.

SFFT

No luck

did you tried patch the game?
without any patch, the game even will have errors with new cards like Radeon 9600 series

I tried it now and it still does the same thing.