Overwriting default Wordpress

This is a website we built for a client on our server which now needs to be transferred to theirs. Our standard protocol is to backup Wordpress files, export the DB, then import the DB on the client's server and restore the backup. This is simply not working here. On the client's server (GoDaddy VPS), every time we try to access the Wordpress dashboard or the front-end, Wordpress installation gets initiated.
However, they are able to install the standard Wordpress installation. And after that, we copy-pasted our files into the folder in which Wordpress was installed, over-writing existing files and then updating wp-config to reflect the correct db parameters. I know this is not standard or recommended procedure but could someone please let me know what are the possible pitfalls to watch out for?