if the problem happens with a project originally released using a previous InstallAware version, some application runtimes have been totally re-designed in IA X3 (as Net, Sql and so on).
I suggest to you to try the following. NOTE!! Make a backup of your entire project folder before to proceed!
A- Open the project and remove any used Application Runtime from the project (Design View in the IDE).
B- Remove any Runtime script eventually left (that refers to the used Application runtimes) in the "Include Scripts" node (left tree pane of the MSI code view in IA IDE)
C- Manually check that any "include script" entry (that refers to the removed Application Runtimes) has not been left in your main script.
D- Finally, re-add all the required Application Runtimes, save and build the project.
The above steps should solve the issue you reported.