Sounds like some of the sites are getting hacked?
In a phpMyAdmin query dialog:
UPDATE wp_users SET user_pass = MD5(‘your_new_password_here’) WHERE user_login = ‘your_admin_OR_user_name_here’
Grab the original (hopefully you have it stored locally) wp-settings.php and upload it to the correct location on the server.
As far as the other blog overwriting the file, you might want to change to multi-sites or ensure the blogs are totally separated in different folders.
This might help.
Settings->Permalinks.
See: http://codex.wordpress.org/Using_Permalinks
