I did not fully understand hatred until I tried to add a religion and ran afoul of the gamefont.tga file. Wow.
My symptom, after moving all the corporation symbols over to make room for the new religion, was that all the following icons were 2 symbols off, in other words the art for Corporation 3 showed on the map for Corporation 1. After hours and hours of trying this and that, I was just fumbling around with an old version of PaintShop Pro and used it to look at the gamefont.tga file. I noticed on close examination that in the pixels where the cyan and pink line pixels were to be transparent on the alpha layer, they were discolored. I made sure to write down the exact pixel coordinates and went into the alpha layer using the DXTBmp software, and made sure those pixels there were the same black as the background.
After that, everything worked. So if you are like me, and have read EVERY thread on this forum regarding that stinking file and still cannot figure out WHY the icons show up on the map in the wrong place..... take the time to make sure the alpha channel is not messed up.