I don't get the problem there. The BIOS disassembly shows a call to 0000:1001 and the source for the bootloader has "ORG 1000H" which means it should be loaded at 0000:1000. Since the first instruction of the bootloader is NOP then the CS: override should be at 0000:1001 which is correct. Your description suggests that it's loaded at 0xfff or the cpu is branching to 0x1002.
