Unfortunately, you are in a catch 22 situation. Since iPage does not allow you to lock your root .htaccess file then you will need to activate Root Folder BulletProof Mode again whenever you save a WooThemes option. The WooThemes Framework uses the WordPress flush_rewrite_rules function whenever you activate a WooTheme or whenever you save any Theme options. The WordPress flush_rewrite_rules function removes/deletes your root .htaccess file code and replaces it with generic WordPress .htaccess code. Since iPage does not allow you to lock your root .htaccess file you cannot prevent the WooThemes Framework from deleting your root .htaccess file code and will need to activate root folder BulletProof Mode again.
*** WooThemes Framework Changelog **
* admin-setup.php - Remove rewrite rules flush in admin_head on each load (now only flush rewrite rules on theme activation and on theme options save).
* admin-interface.php - Added transient (set for 24 hours) to theme version checker, and converted theme update notifier to a WordPress admin notice at the top of the "Theme Options" screen. Flush rewrite rules when saving the "theme Options".