I recently wrote a GUI to duplicate MDT database roles based on the excellent Powershell commandlets written by Michael Niehaus:
http://blogs.technet.com/b/mniehaus/archive/2009/05/15/manipulating-the-microsoft-deployment-toolkit-database-using-powershell.aspx.
Although the Powershell code worked fine when executed directly in a Powershell window, I was seeing mixed results when executing the same code in C# through PowershellInstance.invoke(). Specifically, when I compiled the executable I was able to run the powershell code through the utility without issue, whereas it failed for my colleagues for some reason.

THE FIX

It seems that what I needed to do was ensure that the code was compiled specifically for the platform I was running it on as opposed to ‘any CPU’. In my case this was for x64. You can set this under the project properties in Visual Studio:

However, after making this change, I found I was getting compilation errors along the lines of:
An attempt was made to load an assembly with an incorrect format: [path to exe]

To fix this, I needed to change Generate serialization assemply to Off and everything compiled as expected. More on this here.