I assume the question is why the installation MSI fails when you run it outside of Visual Studio, but works when VS launches it?
If yes, you should first check if your ISLE project is creating an MSI or an EXE bootstrapper (that also contains the MSI). If an EXE is created this is what you should launch manually, not the MSI. In theory, a bootstrapper can act like an initialization support for the MSI and specify default values for certain properties, like an installation folder, etc...
I say in theory because I am not very familiar with ISLE, I work with other setup authoring tools, thus cannot say for sure if this stands for ISE projects too.