I have noticed that this issue has been fixed in the notepad++ plugin. I also updated cs-script to 3.1.17 to see if the command line compile was also fixed but it still seems to be a problem.
If you run: css /cd /verbose RunVirtualDllTests.cs with the sample I've attached it still picks up the file Cache_GetDotNet.cs. If you add some garbage code to Cache_GetDotNet.cs, then RunVirtualDllTests.cs would then fail to compile.
But I don't know if the command line compile is supposed to be fixed yet :)
In notepad++ if I load RunVirtualDllTests.cs then Cache_GetDotNet.cs does not show up in the tree with all the code files, so it all looks perfect in there.
NOTE: I think I've figured out something, don't know if it is expected or not:
If I do a command line compile from the folder that the script is in, it will include all the other cs-script files within that folder.
If I do a command line compile but am not in the working directory then it won't include all other files
This is slightly different than the notepad++ loading behaviour where it won't load the other scripts within the same folder.