Trying to upgrade my forum, but keeps getting this problem when upgrading...

Also the path to the uploads folder has changed in the user part of it.

Is there a way of fixing the problem within FTP or what would I have to do?

Bumping this, still need help on fixing this problem.

Submit a support ticket; best way for IPS to help you quickly 

Have done that. I ended up doing a completely fresh copy of IPS 4.1