So any time you present a user with a UI it will pose some issues with software distribution. The job will wait until there is some user intervention (human initiated or some form of time out). I'm assuming the UI is some form of choice, but could be wrong. Just some thoughts,
So there may be a more glamorous way to do this but, I would just call the batch file with Autoit or Vbscript. This way the package type will not not supress any UI. If you do it this way you can put advanced timers on the batch file. However, if you were going to do that I would just rewrite it in Autoit
RunWait(@ComSpec & " /c " & "yourbatchfile.cmd")
dim shell set shell=createobject("wscript.shell") shell.run "yourbatchfile.cmd", 1, true set shell=nothing
Yes, I am trying to present a choice to the user that they have to input before the install can continue. So with AutoIT, I can put a timeout function in?