Our Buddy!! You're correct. Check the configuration register is the key. The default system startup register is 0X2102. The last 2 is the significant portion 2=0010 in the startup. This tells the system to startup the device normally. check the IOS and then load the config from NVRAM. but the 3rd number 0000 indicates that everything is A OK. If you change the configuration to a 0x2142, you're telling it to start as normal but the 4 indicates that you're not to load the startup up config. This is typically called password recovery mode. If you reboot, even after saving the changes, it will not load them back into RAM from the NVRAM if the register is this way.
So check your configuration-register settings:
use the show version command:
*at the end of the show version output, you'll see the configuration-register that the system has set.*
Then to change the configuration-register:
Router(config)#config-register 0x2102 (to change back to normal startup)
Router(config)# do Wr