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ld -T linker.ld -o $(KERNEL_NAME)

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# Basic Makefile for IBOX OS, Ver.0.01, Date: 04/22/03 1:14PM

# Name of IBOX OS kernel
#KERNEL_NAME = ibox.img
KERNEL_NAME = kernel.exe   

# C compiler to use
CC = gcc   
CFLAGS = -c -Wall -I./include/   

# Assembler to use
NASM = nasm   
NASMFLAGS = -f coff    

# Linker to use
LD = ld   # we're using the GNU linker
#LDFLAGS = -T linker.ld -o $(KERNEL_NAME) # -T, Link with relocation
LDFLAGS = -r linker.ld -o $(KERNEL_NAME)  # -r, Link without relocation

# OBJCOPY
OBJC = objcopy
OBJCFLAGS = -0 binary kernel.exe kernel.bin

OBJS = boot/stub.o kernel/kernel.o kernel/8259.o kernel/exceptions.o kernel/io.o kernel/stdio.o kernel/string.o kernel/timer.o kernel/vsprintf.o boot/handlers.o
all: $(KERNEL_NAME)

install: 
   # this will install the kernel on a floppy
   # you may change this easily
   mount /floppy/
   cp $(KERNEL_NAME) /floppy/
   umount /floppy/

clean:
   rm $(OBJS)

# compile all assembler files
%.o : %.asm
   $(NASM) $(NASMFLAGS) -o $@ $<

# compile all C files
%.o : %.c
   $(CC) $(CFLAGS) -o $@ $<

# and link them all together
$(KERNEL_NAME): $(OBJS)   
   $(LD) $(LDFLAGS) $(OBJS)
   $(OBJC) $(OBJCFLAGS)

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OUTPUT_FORMAT("pe-i386")

ENTRY("_start")
SECTIONS
{
  /* Kernel .text section */
  .text 0x100000 :              
  {
         kernel_code = .; 
         *(.text)
  }
  
  /* Kernel .data section */
  .data :    
  {
         kernel_data = .; 
         *(.data)
  }
  
  /* Kernel .bss section */
  .bss : 
  {
         kernel_bss = .; 
         *(.bss)
         *(.common)
  }  
  /* Kernel .end section */
  kernel_end = .; 
}

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>NASMFLAGS = -f coff    

Try this instead:

NASMFLAGS = -f win32

COFF and Win32 PE COFF object files look identical, but they're not (the relocations work differently).

"ld -r ..." just combines two or more .o files into one .o file, so that's probably not what you want.

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stub.asm compiled to stub.o

objump -d -r -s -x stub.o >dump.txt
Files are attacted below

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ld -v = 2.14.90 20030901
gcc -v = 3.3.1 (Cygwin special)

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LDFLAGS = -T linker.ld -o $(KERNEL_NAME) -lgcc -L/lib/gcc-lib/i686-pc-cygwin/3.3.1