Hi, thanks for sharing this issue.
NCrunch itself is just a console application. It may be worth trying to build your own console application and loading the secrets from there, to see if there is a difference in how it works.
NCrunch has no integration with dotnet secrets, and I confess that I have no experience in working with it. Is it perhaps possible that the system is sensitive to the directory your code is run from? NCrunch will run your tests from a separate workspace which might affect this.