I just bought Red Faction for steam, having played years ago and finding it a very enjoyable game.

However I have an issue when using headphones - sound effects don't work. I can hear the music but can't hear effects such as gunfire and also voices.

I have tried using pure faction but the issue is still there. The problem doesn't happen when using my speakers though.

What kind of headphones? Some USB thing or plain old analog?

What does your audio config look like in windows? Stereo or are you doing surround?

Maybe try toggling the EAX option in PFLauncher.

Also can't hurt to do a test like this:

with that video is it normal for the first left part to be quieter than the right part
or should both the left and right parts should the same

I would presume your balance is off. You can edit this under the sound device options.