I have had a PMR open for some time relating to a bit of a known issue with Custom themes and Connections communties
There was an issue where you would create a custom theme
In my case I also customised the coloured community themes also
Step 1.d – d. Remove the file theme.css from the corporateTheme directory
In my case I had based my custom theme on the default theme and had used it as the default Community theme (which has no theme.css), so all communities with the default theme appeared correctly.
BUT, I had also lightly customised the coloured community themes – removing (or renaming) the theme.css from each coloured theme has resolved the issue.
Thank you mr Kieran Reid for investigating and confirming this was the issue.