What's your current config-register status ? 0x2102 boots the config in the nvram where 0x2142 boots into the setup mode and it will deny any config in the nvram at that moment. My assumption it can't find a decent config in its boot sequence and it starts to look for a tftp server and get some configs from there.

Try to set the register to 0x2142, that way it never tries to find the startup-config and goes directly to the setup-questionaire ...
If you need to reconfigure that much i'd copy a default config to the startup, reset register to 0x2102, and then only play with the running-config itself. you can erase that one as much as you want, as long as you don't copy the running to startup you'll always end up in a nice default env.

Hope this helps,

PS: Post 1000. YAY !