Some vendor provided MSI packages may insist on being run from a setup.exe. This is to ensure that the latest version of InstallShield Script is present on the system. This too is an MSI, so deploy it separately and then make one of the following changes to stop the MSI from checking to see if it was run from its setup.exe file...
1) Add the property ISSETUPDRIVEN to the command line (or via an MST by editing the property table) and give it a value of 1.
2) In a transform file, add a condition to the "OnCheckSilentInstall" custom action in the InstallExecuteSequence so that it will always resolve to false or remove the custom action from the sequence.
NOTE: There is feature introduced with AdminStudio 6.0 that attempts to convert InstallScript MSIs into basic MSIs, click here for the part of the AppDeploy review that discusses this feature. Be warned though, this feature has issues in detecting InstallScript packages and in generating proper output when it does- use with caution.
For a detailed video discussing and demonstrating all of these methods, see Dealing with InstallScript for Administrators.