For anyone else having this problem, I figured out what was wrong (although I am not sure why it caused a problem). For clarity it wasn’t that only 1 recommended product was shown, it was always 1 less than was specified.
I had unchecked “Override theme’s template” as I wanted to use my themes markup and styling. There was a filter in my functions.php file for woocommerce_output_related_products_args which changed the posts_per_page argument to -1 as I wanted to show all related products (in my own slider). The problem was caused by this setting as setting it to an artibary number i.e. 18 made the correct number of related products be shown. Obviously now I am only showing a maximum of 18 products but that is plenty.
