You're definitely on 1.001 from your error messages, so...
Is it saying it can't write to a file, or can't read a file?
Are you hitting Download Updates in the game version 1.001, and is that working? If you just hit "run manually" it won't have downloaded anything to run manually against. So far as I know, the updater is working just fine in 1.001, and you seem to be on 1.001, so I'm not sure what the problem with it is.
If the above doesn't help, can you walk me through your process and what the error is? Sorry for the trouble here, that is most odd.