DTSInstaller.exe consumes a file called with an extension of SSISDeploymentManifest
The contents of it look like
That file defines the universe of SSIS packages the DTSInstaller will operate upon.
It sounds like the manifest file you are using does not have match the list of packages in your project. You can right click on the project itself and select Properties, Deployment tab and change the value of
CreateDeploymentUtility from false to true.
Now when you right click on your project to build, or deploy, your bin\Deployment folder will contain a new version of the manifest file. Double click on that and you should have all the desired packages ready for installation.
An alternate approach, would be to use your manifest file but have PowerShell generate the deploy commands. Advantage of that is you can audit what's being deployed versus the black box of DTSInstaller.exe PowerShell, dtutil, SSISDeployManifest - How to deploy SSIS packages with PowerShell