Loading configaration problem

[Paul f]

I am having a problem loading a configaration file .What is happening is I flash the chip with the bootloader using a seperate programmer and then fit to megajolt.I can connect and see the basic configaration and the run time screen is operational with a map sensor reading that changes if i suck on the pipe from it.As soon as i try to load a configaration or change any value in the map table I am unable to comunicate with the chip any more.
If I put the chip back in my serial programmer and erase and then reprogram it, the process repeats.I am now really stuck with this and have been trying for a week now to get it to operate correctly.
Can anyone please suggest what i should check for?.I have linked the pins 11 and 12 of the processor socket with it removed and get loopback with hyperterminal but dont get anything when the chip is installed.
Paul.