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My system specs are as follows :
GPU - GTX 750 M (1G)
CPU - Intel® Core™ i7 4700MQ CPU @ 2.4Ghz
Resolution - 1399 x 768 @60hz (with current driver)
OS - Windows 8.1

I have been successful playing other games with no issue. I am mounting my files instead of playing from disk. My other games load no problem, but when I try to load MGS2 Substance the play screen remains blank......
I am new here so I apologize if I broke any forum rules, thank you.

By "mounting my files" do you mean with something like Daemon tool/magic disc?

If so, don't do that. Use the internal built in ISO loader.

Additionally, please show full emulog after the problem occurred.

Taken from my test result on the Wiki.

Quote:BIOS: USA 2.30, Takes a while to start up due to being a DVD9. Requires a powerful computer to run at fullspeed, and even then there's still some slowdowns. Also requires fiddling with sensitivity on controller settings as well if you want to properly play this game. (When holding up enemies, etc). Pressure-sensitive controller recommended!

Give it some time. It has to check the extra layer.