I hadn't checked in a while, hoping there would be a fix for the issues I had with the game. And while the D-Pad issue has been addressed (THANK YOU!!) There is still a problem with a certain sound effect.

In the original MSX version, when you pull up the radio/codec to call one of your contacts, a tone plays that raises and lowers in pitch, repeating until you exit the screen or place the call.

There are two issues with the sound effect in the GOG version, one is that the sound effect doesn't loop, the other is that the actual sound that is playing sounds like a cartoon sound effect and has a completely different feel than the original.

This is the file that sounds completely wrong. I assume it would be a simple matter to replace this file with a proper sounding one.
...\Metal Gear\Sound\mg1_se43_musen_search.wav

The original sound was like this file, only the longer version
...\Metal Gear\Sound\mg1_se03_musen_res.wav

This short version plays when you receive a call, before the text of the message starts to display.

Fortunately, all the other sounds in that directory seem to be correct.

I haven't played very far because I find this issue incredibly distracting, and it's a sound effect that you hear quite often. It may be a minor issue, but it's a noticeable one. I hope this is corrected for everyone to experience a more accurate game!

Yeah this pc port is strange in many ways. It is basically an up-ported cellphone (pre-smartphone, java perhaps) game. Aside from the sound anomaly you mentioned above there is also some weird pre baked reverb on all sound files, you'll also notice that the gameplay is choppier than on the MSX as well. On the plus side the new translation contains all of the tansiever messages that were removed from the original English version. There may be discrepancies on how the guards behave too though I'm not certain.