Magento – Paypal express shipping methods

Assuming you cleared cache, flushed apc/OPcache (if in use), ran compilation process (if in use), here is a small list of things to check:

1. Check if all 1.9.1 files have been copies over
2. Open app/code/core/Mage/Sales/Model/Order.php and look for queueNewOrderEmail method
3. If the method does not exist you don't have latest file
4. If the method exists check if some third party module is rewriting the class and check your local code pool for override of the given class

Source: Here

I think the issue here is that this can only be turned on/off at a website level.

If you go to the admin config and select the website you want to turn off the express checkout then when you go to the Paypal Express configuration you will see the field Enable this Solution. Here you can set it as No, save the config and clear the cache then you should not see the express checkout option anymore.