It's hard to say whether there is a connection between the need for a manual install and the problem described above. At the moment both of these problems do have two things in common - neither has been reproduced in an environment where they could be fixed, and both are caused by unknown constraints that are present in the install environment.
The MSI contains a pre-condition that checks for the location of Visual Studio before running the installer. This condition checks the registry for the value defined in HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\VisualStudio\11.0\InstallDir (or alternatively under the Wow6432Node for 64-bit installs). If for whatever reason this registry key can't be accessed by the installer, it will fail. My suspicion is that this could be blocked by a virus scanner or security restrictions in the O/S, although I've never been able to create an environment with configuration that could cause this to happen.
In the case of the Gallio.dll resolution issue, I'm quite certain that this is also caused by a constraint in the environment which is abnormal. In this case we have two normal co-located assemblies being loaded from the same directory, and one cannot find the other. I suspect this to be caused by one (or more) of the following:
1. Unusual configuration of the machine (i.e. machine.config or CLR configuration at some other level)
2. O/S restriction perhaps caused by security constraints/permissions issues
3. Virus scanner or third party software that is interfering with the assembly resolution
Provided the manual install is done per the
instructions in the documentation, there shouldn't really be any functional difference between the MSI install and the manual install. NCrunch itself is just an xcopy installation - with an additional step to flush the VS extension cache so that it will find the addin.