Yes, I guess it is two separate issues. Your description of both issues is accurate (let me know if you want me to split them into separate posts).
Regarding the solution switching configuration UI issue, I managed to reproduce this quite easily:
* I created a new Class Library project in C:\A\ClassLibrary1.csproj and added NUnit via Nuget and an empty test fixture and test method
* I configured the project with 'Additional files to include' and just pointed it at my Nuget package.config
* Everything built and NCrunch detected the test and executed it.
* I copied the .sln, .csproj, .cs, .config and Properties folder to C:\B (no NCrunch files were copied)
* I closed ClassLibrary1.csproj from C:\A and opened the identical one from C:\B
* I enabled NCrunch and when I went to configure it, my additional file was already there in the configuration UI (the UI shows it despite the relevant configuration not being present in the .v3.ncrunchproject).
Regarding the 'Project config file storage page'. It doesn't seem to matter what I set it to, nothing ever gets written to the path. The files always get written beside the project files.