What are you using to build your image with, and how are you applying the new image?
Depending on your dashlaunch settings, easiest way to get to NXE from FSD (for me) is to press the guide button, and scroll over to system settings. You could always change your dashlaunch ini if system settings aren't displayed in your hud.
If NXe isn't working, you must have bad blocks being remapped incorrectly, or not even being identified. More likely Newbie error in how to get to NXE in my opinion, but not after rereading your post. I'd definitely go with bad blocks. Do you have a hardware method of dumping your nand? If you have a backup of your nand, from the very first time the machine was modded, you could identify the blocks with it, but it'ld only help with old ones. If it's been a while it's almost a certainty you'ld have those plus more by now. Flash memory always gets bad blocks with time.