It has been four weeks with no answers ... so I finally figured this out on my own. I hate answering my own questions, but here it is:
The SUO file is where all the settings, startup project, and cached user options are kept. With large projects there are times where the .suo file becomes corrupted or too large causing sluggish, or odd behavior with these options. Case in point the outlier I ran into with my open classes not being remembered.
Solution: Simply delete the .suo file. Visual Studio will create a fresh one for you. I did this and it solved the problem.