CorvusFortis... The Main problem is the popupborders.pcx has the transparent colors in the wrong palette slots... they go at the end.
The PopUpand MenuBackground.pcx is OK with leaving the Transparent slots as Black because there is no pure Black in the image. That said it is a good idea to place the same transparent colors as is used in the original file.
Generally, it is best to use a texture image for the popupborders.pcx that will not matter how the tiles are placed together in the game.
If the images you are using are what you want, these files should correct your problem.