I managed to fix the problem with the colors. I changed the transparent colors to bright red and green, and used it for a reference to change them (In MSPaint no less!) Now I got a tileset that compiles fine with no color loss.

Thanks guys. The learning curve was a little steep (Mainly because I had to download two 20mb applications to play with the images. --Dialup. ) But now it looks like clear sailing here.

Iconguy, there is a direct link to DTR in the JCS section of J2O, so it's just two clicks away.