I solved the problem, but it may be caused by a bug.
Minishop2 saves the paths to the files in the database relative to the host, not the modx install's root. So if your developing in a sub directory then the folder will be stored in the path too e.g.
/developmentarea/subdirectory/assets/images/products/249/120x90/test.jpg
Thus breaking the links when the site goes live.
The tables holding the path were
modx_ms2_products and
modx_ms2_product_files.
I exported the tables then opened in a text editor and corrected the path by removing
/developmentarea/subdirectory/
leaving only
assets/images/products/249/120x90/test.jpg
in the table. I then imported it back into the database which meant image source was correctly linked to the modx install.
With help from @nadakbar.