Targetless Compilation Issue

I am having problems with the targetless compilation. The .bin file created using the targetless compilation is slightly different from the .bin file created using the compile to .bin using attached target option. In fact there are 14 places in the file where it is different. For the most part the difference is unnoticed. However I am using the shdesigns Ethernet downloader to update the software over Ethernet. When I create a .bin file using the attached target everything is fine, but if I create a .bin file using the targetless option the downloader no longer works.

Is there some way to tell what is causing the .bin files to be different? From what I can tell I’ve selected the correct board in the board selection tab. We are using the 58MHz RCM4200 boards with 512K+512K SRAM, 512K Flash, analog, and 8M serial flash