Just to follow up on my own question, it appears to be a bug in the new graphics engine, so I will stick to R2014a and hope that they fix this in R2015a. I received the following response from the MathWorks Technical Support Department on 11/24:
Thank you for sending all of your reproduction information. I was able to reproduce the behavior you were experiencing and confirmed with the graphics development team that this is a known issue in R2014b that they are actively investigating.
In R2014b, there is no known workaround. The best recommendation I can offer is to plot markers at the endpoints of the lines by setting the 'Marker' property in the 'plot' call so that there will be some visual indication of the correct length.
I apologize for the inconvenience this issue is causing as well the extended amount of time it took to reproduce the issue and get back to you with a conclusive answer. If you have any further questions, please let me know and I will be happy to assist you.