Final Cut Studio 3

So I'm creating a package of Final Cut Studio 3 using Composer 7.2. The package was created on a bare image which included all the updates I expect to put into it. It's gone pretty good for the most part except I've noticed something rather strange when the image is created. When I use the package in InstaDMG, I log into the admin account (which was created using CreateUser.pkg) and I notice in the Admin account folder all sub-folders are missing. I'm talking about the Desktop, Music, Pictures, etc folders. I've tested this by opening the dmg created by InstaDMG. The odd thing is that when I boot into the image, it will then create the Desktop folder. This seems to affect the Dock as well. The standard alias on the far right side which point to the Documents and Downloads folder are suddenly question marks (clearly because it can't find the Documents/Downloads folder). This is a stark difference from the environment that was used to create the image. I thought originally maybe there was something wrong with the other packages I was using, but when I leave out FCS, the image seems to work fine. When I include FCS3, these oddities start to appear with the aliases and the missing folders. And lastly, when I used Composer to create the Final Cut Studio package, I made sure to include the two updates that came up in Software Update. However once the FCS package is included in the image, I notice that I am prompted to install the ProKit Update 6.0.1 which doesn't make sense since I included it in the FCS package I created. Any ideas on what could be causing this? What a nightmare it is to package it. I can only test once a day to see if this works because the software itself is like 46GB packaged up. I'm not sure what else to do at this point.