So we approached MPC via a ticket and this was their response:
"Flipbook is using serialized array (http://php.net/manual/en/function.serialize.php ). Simple search & replace method, while transferring Flipbook settings is not enough. The data are saved as a serialized array. This method include a string length parameter inside the saved data. So, this value has to be adjusted after changing the string length (for example domain name)."
And they recommend the following steps which worked like a charm.
Before you proceed to remember, backup your backups and then try this out:
These steps did it for us. And now everything works just fine.