msi vs. exe doesn't create a difference.
in your deployment properties, regardless of what you are deploying, there are choices to be made there; about whether or not that particular deployment should be visible in Software Center. Look at the properties of the two deployments.
Take a look at this link for a good explanation of what shows in software center and when:
It comes down to what you are deploying and what type of deployment. Also look at user experience settings on the program.
Jeff
Here are the settings on the Package deployment (.exe) I do not have any setting that says "allow running on Software Center" Where is that?
there is such a setting. This is from Jeff's link. this is only available on applications, not packages. how come?
Because the application model is completely different from the old package/program paradigm.
Jeff
You'll have to troubleshoot that as this is not normal.
Have you refreshed the machine policy?
Have you reviewed the logs? Like policyagent.log, policyevaluation.log, and execmgr.log?