I have the same issue. The last large deployement I did, there were a small percentatage of machines that had this issue. It was originally a .vbs package, so I thought there was a problem with wscript, so I created a batch file, then tried creating an exe created using AutoIt. Nothing worked. I opened a ticket with out TAM, but it was never resolved. This was on 8.8 SP5.
Well, I am glad that I am not the only one with the issue. I have been going crazy trying to figure it out. I am relatively new to LANDesk and thought I was just doing something wrong.
Today I tried running with just a status bar. The msi kicks off and status starts to progress but only stays up for about 5 seconds. I then tried running with a full UI and it launches but when I go through the install, the screens are different from when I run it manually. Very strange....
Aparently there was an issues with the actual msi itself which was causing this.