Do you trust your code? your compiler?

Erik is correct.... If this is the 1st part you have programmed with the programmer... get some "simple" assembler code to turn a port pin off/on.... Oh, remember the LPC900 I/O is not default quasi-bi-directional, BUT IS DEFAULT input Hi-Z impedance.
-- Hence you will need to set PxMy port configuration registers (ie P0M0 = 0x00,,, etc).


BOOTSTAT
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The BOOTSTAT is BSB is set by hardware to allow code execution from the user code (0x0000) or the default bootloader (unless you changed the boot loader vetor address)..... this is for the ISP bootloader (probably not ICP).

BSB is set by hardware either by ISP hardware entry method (3pulse on reset after power up) (or AUX UART break signal). On reset, and BSB =1 the LPC900 jumps to the ISP bootloader.... ready to receive programming commands down the UART.

My educated guess is the programmer uses ICP which is the lower level hardware programming method than UART driven ISP.

So for ICP programming low level programming my other guess is BSB and the BOOTSTAT is not used or needed. The LPC900 should start executing user code at 0x0000, if the BSB is un effected by external hardware influences (or AUX UART break signal).

If your programmer is verifying the part is programmed OK, then it may be something other than the programmer... (but keep it under suspicion).

Regards
Joe