Thanks for the welcome and the help!
I did some more testing and unticking "Enable OpenCL compute acceleration" certainly did help with the black square issue.
Unfortunately, while Affinity Photo is working the batch job it seems to really slow down my system. I tend to batch job a lot of images so usually I work on something else while this happens but this makes it a bit harder to do. The slow down does not happen with OpenCL ticked. Either way, this seems to be a hardware issue so as far as my issue in this thread is concerned, it is solved. Thanks!
On a side note, before you replied I was trying doing batch jobs with "Parallel Processing" unticked and this seems to also make the black squares go away but at the cost of a significantly slower batch job.