I was able to get team symbols to display correctly everywhere (in the interface, on flags, banners, video screens, etc) by importing them as masked images rather than alpha'd images.
Instead of creating a .tga (or other) file with an alpha layer, I instead created an 8bit (greyscale) .bmp file. The team symbol was white on a black background. When I imported into UnrealEd, I selected masked (instead of alpha'd), and everything seemed to work dandy. Important note: things only seemed to work if the image was an 8bit greyscale image. When I tried importing a 14bit or 32bit RGB or a 2bit bitmap image, things didn't go so well.
I hope this helps someone!