1. Open config.cfg using Notepad or Notepad++, change the seta "v_windowed" "1.000000" to seta "v_windowed" "0.000000" and open DOOM64.EXE.
2. Then (In the Game) go to Options > Video > Change the (4:3) to (16:9) in the Aspect Ratio. Then change your resolution (I use 1280x720), Close and Open the Game.
Well, at least this is the way i fixed it. I decided to post this because no one has posted how exactly to fix it yet.
Thanks D88M for the tip in this post