Re: USB Device Bootloader problem
The two entries shouldn't be a problem. As long as the very first code (crt0.s) is in the 0x9d001000 area, then it should be fine. That's because the linker puts things in from largest to smallest, other than the first thing that is run, which is crt0.s.
Have you been able to debug the application at all? By having the bootloader project as a loadable to your application project, you should be able to go through the bootloader and debug from there.