Sounds as though your Xbox is softmodded and has virtual eeprom enabled. You need to temporarily bypass the virtual eeprom to make the changes, otherwise you aren't changing the real settings, just the temporary ones in memory. How you do that depends on your softmod. For Krayzie NDURE you run Krayzie Extras, for Kingroach you run E:\ndts\default.xbe. If you aren't sure which softmod you've got, boot with Frosty's Rescue disc - that also bypasses the virtual eeprom - then select Rescue Applications - Xbox File Manager and run xb0xdash.xbe. In all cases unless you have changed the default settings the LED will be red when the virtual eeprom is bypassed.
For this to work properly you need to ensure that you DON'T have a copy of eeprom.bin on the Xbox. If you have then make sure you have it backed up to your PC, then delete it from your Xbox. You might have to bypass the virtual eeprom to do that as well.