I'm pretty sure defaults are empty files.

If Fn doesn't lock it's a software problem, not a hardware issue, seems to me. Perhaps a backup and a complete reflash would fix the issues. I'd recommend and backup to SD, then wipe the OS with a flash and then the user space.

Once it's up and running, start re-installing apps and rebooting, see which does it. Maybe you installed something that remaps keys in any way, or at least uses a library that does this, intentional or not.

Low on ideas on this one. Best I can tell it's not a hardware issue as the Fn lock is handled in software (it doesn't work in MicroB). So, since it works on a new N900 and has since stopped, I'd venture a full clean would do it. Make sure it's full, there's a full guide in the wiki,