This was caused by user error. I worked with Deakcor this morning and got this sorted out.
What had happened is, I had changed the file structure of my video game project. To better organize my images, and other files. I hadn't realized that PixelOver launches it's project files, from using the original source files. Whether it is multiple static frames to create an animated image, or a single frame of an image being added to an animation within PixelOver.
All I needed to do, was open my .pixelover project files in Notepad, or in my case Notepad++. Then replace the file locations with the proper directory paths on my hard drive to the source files for each project. Now, everything is loading up perfectly in version 0.10.1.1
Thanks again, Deakcor, for all of the help, and working with me to help get this resolved this morning!