I'm merging two tables but the source is the same, i.e. another PBI dataflow. I've since isolated the issue to an unpivot of columns and I've just implemented another solution rather than doing the unpivot. Which has worked around the issue.
I may revisit the unpivot solution at a later date to see if I can resolve it but as it stands it not worth investing more time at the moment since its working and the query takes around the same time to process.