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(I bet this is something stupid.)
I programmed an LPC2458 successfully with a small hex file using the GUI, but when I tried the same using the command line, the operation appeared to succeed, but the memory was unchanged.
Here's a log of what happened.

C:\...\test>"\Program Files (x86)\Flash Magic\FM.EXE" COM(9,115200) DEVICE(LPC2458,12,0) HEXFILE(tmp.hex,nochecksums,nofill,protectisp)
Flash Magic Version 6.93.2767
8051/XA Driver Version 3.02.2727
ARM UART Driver Version 3.03.2727
ARM Cortex UART Driver Version 4.01.2767
ARM Ethernet Driver Version 2.02.2727
ARM Cortex Ethernet Driver Version 2.04.2752
ARM CAN Driver Version 2.03.2727
(C) Embedded Systems Academy 2000-2012 All rights reserved
NON PRODUCTION USE ONLY
Connected
Device selected
Hex file programming complete (tmp.hex)

C:\...\test>"\Program Files (x86)\Flash Magic\FM.EXE" COM(9,115200) DEVICE(LPC2458,12,0) READ(0x7cff8,0x7cfff,read.hex)
Flash Magic Version 6.93.2767
8051/XA Driver Version 3.02.2727
ARM UART Driver Version 3.03.2727
ARM Cortex UART Driver Version 4.01.2767
ARM Ethernet Driver Version 2.02.2727
ARM Cortex Ethernet Driver Version 2.04.2752
ARM CAN Driver Version 2.03.2727
(C) Embedded Systems Academy 2000-2012 All rights reserved
NON PRODUCTION USE ONLY
Connected
Device selected
Flash read complete (read.hex)

C:\...\test>fc tmp.hex read.hex
Comparing files tmp.hex and READ.HEX
***** tmp.hex
:020000040007F3
:08CFF80001000000010000002F
:00000001FF
***** READ.HEX
:020000040007F3
:08CFF800000000000000000031
:00000001FF
*****
C:\...\test>