There is a previous thread about this subject here: www.red-gate.com/MessageBoard/viewtopic.php?t=16319
Although it's not ideal, the advice was to use Microsoft.Web.Administration rather than the WebAdministration module (see http://www.mattwrock.com/post/2011/01/0 ... ssues.aspx
However, it may be that the next release of Deployment Manager will remove the need for you to add custom powershell at all because it will include functionality to create IIS applications.
Basically, if the web application does not exist on the Deployment Agent when it's package is deployed, then it will be created in IIS (the web app will default to being on port 80, but this can be overridden with a variable). Does that sound like it will meet your requirement?
This next release should be out in the next week or so and will be announced on this forum.