Lpc2000

Hi,
I use the LPC2148 with Jlink IAR.  I use debug flash in the IAR setup,
so that when I unplug the JLINK the code is already flashed in the
part.  I tried to create a hex file in IAR using extra output in
linker options, and Intel-extended format.  It seemed to work, but
when I use the Philips flash utility, the code seems to run a bit
differently (display glitches sometimes P1.16-P1.23).   
Might I be producing the hex file incorrectly, or might some other pin
functions be activating that the JTAG supressed?
Running with the JLINK flashed part runs fine, it's just a hasle.
Thanks for any ideas.
Steve