...answering my own question...
It seems that if your column is at the end of the field list in Excel it won't merge.
The order of my columns in one of my Excel sheets was a few Dimension columns, then Measure columns and then the last column (which I was tring to merge on) was another Dimension.
Seems like Lumira doesn't like this when attempting to merge. Whatever I put in that last column it wouldn't merge.
In the end I copy/pasted that column so it sat next to the other Dimension columns in Excel; then re-imported the data.
When I tried to merge this time worked fine