Workspace File won't deselect in Deployment Utility.

[ShockHouse]

I've been working on a deployment for a computer this week. I've ran into some issues with the Deployment Utility that I have not seen before.

My computer has TestStand 2014. LabVIEW 2014 SP1.

One of the issues has to do with my workspace file (.tsw). For some reason in this specific deployment the .tsw is always being selected. Normally I can unselect it, save the deployment and it will stay unselected. On this one I will unselect it, save it, and it will select itself again. It will select itself if I move from 'View Build Preview' to 'View Source,' if I analyze again, or sometimes if I go to Installer Options or System Source. The problem this causes is when I go to Build. Since the Build analyzes again it will select the workspace file and include it in the Image and Installer. That is something I don't want to happen but I can't find a way to keep the .tsw unselected.

The other issue has to do with how the paths are displayed in 'View Build Preview.' I'm not sure if this is causing an issue, but one of my source files is showing up twice (MD5Checksum.llb) even though it is only used once in my sequence so it may be caused by this. Normally when I go to 'View Build Preview' the top folder will be the Installation Directory. That will be followed by all the paths to the source files used by my sequence in the workspace. It will normally look something like this:
Installation Directory/C:/Folder/Folder/Projects/Folder/*.vi
Instead it looks this in the deployment:
Installation Directory/Projects/Folder/*.vi
(This is without me moving anything or touching anything yet, this is after the first analyze of the source files).
Another example is that I am using Unzip.vi that is part of LabVIEW/vi.llb. Instead of showing Installation Directory/C:/Program Files/National Instruments/LabVIEW it shows Installation Directory/Projects/LabVIEW/vi.llb/zip/Unzip.vi
I don't even have a LabVIEW folder in my Projects folder so this path isn't even relative, it's a path to nothing. Underneath File Properties on the right it shows the correct full path for everything.

Both of these issues are what I am seeing at face value. It's causing issues in that I can only get a build to work one out of every 100 attempts. During the build if it fails it gets all the way to make an installer, says there was an error but doesn't say what the error is. I'm hoping if I can fix the two above issues that I should be able to fix the rest. If any of you have come across these what did you do to fix it, or where should I start looking?

Thanks