The copying of content files takes into account the project dependency tree, which means that if your main project depends on any other projects that contain content files, then these contents files will also be copied. Does your main project depend on any other projects in your solution? Perhaps one option could be to try setting your sample test project to point at different projects in your solution .. maybe this will help with narrowing down the issue.
I've been digging in my brain for a way we can analyse this issue, and I'm wondering if you might be interested in trying a new build. The 2.5.0.6 build below contains several changes that I think will help us here:
1. This build will now report the files copied in its trace information. If you turn on the 'Log to output window' global configuration option, and set the 'Log verbosity' to 'Medium', watch out for the messages saying: Copying content file X to windows store sandbox at Y. This won't tell us which files may be messing up the sandbox, but it can provide extra information that could prove useful. These details will also be included in any bug report you send to me from this build.
2. You can now entirely disable the copying of content files by setting an environment variable on your machine. If you set 'NCrunch.NoContentCopying' equal to '1', NCrunch will avoid copying the content files. It's a bit of a hack, but should help us with confirming whether there was another change in 2.5 that has caused a problem. If you try this and the build still doesn't work, also keep an eye out in the log file just to make sure the files aren't being copied and the environment variable has had the intended effect.
3. I've adjusted the sequence of file copying into the sandbox to reduce the risk of clashing between the projects. Although I haven't isolated any situations where the previous method would create a problem, the Windows Store sandbox contains many surprises and the new approach is likely to be safer anyway.
Something that may also be worth trying is comparing NCrunch's Windows Store App sandbox with the one usually created by VS/MSTest. If you right click on the failing test in the Tests Window, then choose Advanced->Browse To Workspace, look for the NCrunchAppx directory underneath the project's build outputs. This directory should be fairly similar to the Appx directory created by VS/MSTest when they run your tests normally. There'll likely be a few obvious differences (such as NCrunch DLLs instead of the VS ones and references to these in the package manifest), but the rest of the contents should be more or less the same. Do you notice any big differences that look out of place? Particularly around content files or package manifests?
http://downloads.ncrunch.net/NCrunch_GridNodeServer_2.5.0.6.msihttp://downloads.ncrunch.net/NCrunch_GridNodeServer_2.5.0.6.ziphttp://downloads.ncrunch.net/NCrunch_VS2008_2.5.0.6.msihttp://downloads.ncrunch.net/NCrunch_VS2010_2.5.0.6.msihttp://downloads.ncrunch.net/NCrunch_VS2010_2.5.0.6.ziphttp://downloads.ncrunch.net/NCrunch_VS2012_2.5.0.6.msihttp://downloads.ncrunch.net/NCrunch_VS2012_2.5.0.6.ziphttp://downloads.ncrunch.net/NCrunch_VS2013_2.5.0.6.msihttp://downloads.ncrunch.net/NCrunch_VS2013_2.5.0.6.zip