Could you please enable the Path hint in admin. Double check the all phtml files having the key code in your template files
<?php echo $this->getBlockHtml('formkey') ?>
Please double check in the following files.
Shipping cart form:
app/design/frontend/<package>/<theme>/template/checkout/cart/shipping.phtml
Multishipping billing checkout form:
app/design/frontend/<package>/<theme>/template/checkout/multishipping/billing.phtml
Multishipping shipping checkout form:
app/design/frontend/<package>/<theme>/template/checkout/multishipping/shipping.phtml
Billing checkout form:
app/design/frontend/<package>/<theme>/template/checkout/onepage/billing.phtml
Shipping checkout form:
app/design/frontend/<package>/<theme>/template/checkout/onepage/shipping.phtml
Payment checkout form:
app/design/frontend/<package>/<theme>/template/checkout/onepage/payment.phtml
Shipping method checkout form:
app/design/frontend/<package>/<theme>/template/checkout/onepage/shipping_method.phtml
Persistent Billing checkout form:
app/design/frontend/<package>/<theme>/template/persistent/checkout/onepage/billing.phtml
For More Reference
Security Patch SUPEE-9767 - Possible issues
Note
You can use git private repository for handling the codes. it would be easy to revert the files