I had something like this happen once before. The MST had a reference to a Network locations that the System did not have rights to. I may be way off base here.
In my case it was ZenWorks, but I assume they install applications the same way. The installation takes place with System Rights. If you for example writing a log file to a network share that did not have Domain\Users privledges that could cause this sort of thing.
I don't know if this helps may it is worth looking at though.