Tom
You will need to give some more info before continuing :
1) what is your target board and processor
2) what tools are you using (grennhills, gnu, etc)
3) how do you connect to your target board (angel, JTAG, etc)
4) when you say that "I download program to board" - what are you using to download? how ? - as much detail as possible
5) when you say "I run the program in the debugger tool" - what are you doing ? as much detail as possible
The impression I got from your origional mail was that you have some target board that you are able to run your program on when you use an In-Circuit debugger, and that you are having problem running the program when loading it raw (e.g. through a bootloader). Maybe I made too many assumptions?
Simon