I’m seeing some odd behaviour I can’t explain.

I'm using wix to generate a msi and using the msbuild GenerateBootstrapper task to handle pre-requisites. It all seems to build correctly i.e. there are no error or warnings but the generated setup.exe won’t run. It gives a nice blank error dialog and the event log gives about the same information.

The kicker is that if I drop to the command line and run msbuild manually on the project and specify the bootstrapper target it generates a correct and working setup.exe.

I've used this wix article as a base and a number of questions on StackOverflow to no avail. Has anyone seen this behaviour before, better still a fix?