<p>We are trying to automate a build of one of our products which includes a step where it packages some things with WISE.  At one point WISE pops up a window with a progress bar on it to show how it is doing.  If one is connected to the machine with remote desktop the build works fine but if one is not connected the build stalls until you reconnect at which point the window opens and the build progresses.  Does anybody know of a work around for this?  Some way of tricking windows into believing that there is a desktop session connected?  </p>

What version are you using?  Looking at the feature set, it looks like their "std" version might be limited.  Perhaps unattended installs require the Pro version?
That's just a guess....
Regardless, I wonder whether you could simply code up an auto-run task for the box that calls
CreateDesktop
to pretend there's an interactive login?
I found a
CreateDesktop example
that's about desktop switching, and
an example about unattended installs
-- you might be able to use one of them as a starting point to "fake out" WISE :)
It might be worth a try...