Sounds like your router has an incorrect Config Register setting. From the console, do a "sh ver" and look for the line "Configuration Register is 0x2102" if it is set to anything other than 0x2102, the router will not perform a standard boot. To remedy, go into global config mode (conf t) and issue the command "config-register 0x2102" and then reload the router (no need to do a copy run start). This boot mode will tell the router to load the startup-config from NVRAM at boot and not ignore it. Chances are that the config-register is currently set to 0x2142 which is the mode commonly used to recover a lost enable password.
Hope this helps.