all settings lost after boot?

I was setup with maximizer and keymaps, and after a reboot today all my settings are gone. Has anyone seen this before? I will be sure to back up this directory if I can get it all set up again. I just can't imagine what could have deleted them. I would not even know what the filenames would be for the configs other than the keymaps.

Also, once everything is set up, how can you skip the startup command and not start everything? Like if you want to edit or add keymaps or change some other setting.

Thanks,
-K