I've upgraded from Magento CE 1.6.2.0 to CE 1.9.3.1, but did so with the following command: ditto -V path/to/magento/1.9.3.1/ path/to/magento/1.6.2.0
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After putting this live, there was an error when going to System -> Configuration (blank page), as described in this article section. So after reading this I found out there were a lot more files that didn't get deleted, so I deleted and replaced the src/code/core and src/lib directories to be on par with the actual upgraded version.
Everything so far works as expected, but now I can't create a customer, or change the password for an existing customer (both from customer account as in backend). It fails somewhere with handling the password. I've been able to trace it back to the createPostAction and editPostAction within src/app/code/core/Mage/Customer/controllers/AccountController.php, but I'm stuck there.
Has anyone come across this before and how can I fix this? Many thanks to whoever can help me.
Note: I now this is not the normal way of handling upgrades, but this was the only way availeble for me (Magento Connect is disabled). I've also checked the template file, as described here