I am having an issue with a really large install. I am trying to create a MSI with a Cab next to it that contains all of the other files. Everything I try just creates all of the install files next to it (no cab).
Can you please make sure you have selected the "MSI with resources next to it" package type option from "Builds page -> Configuration tab"?
It will be useful for us if you could isolate the behavior in a small buildable sample (AIP + its referenced files) and attach it here so we can fully analyze your project settings.