Andy,
I probably won’t be able to help, but I can do some testing locally and see if I can find anything to help. I do have a .NET 6.0 web app set up running Hangfire, but it’s running at the root level. Can you let me know how you have configured your .NET 6 app to run as a sub-application? Are you only doing this on the server (in IIS) when you publish/deploy the app, or do you also have it set up to run as a sub-app in Visual Studio?