Double sun images in HDR

I have recently started to take some landscapes and seascapes using the LR HDR link with Photoshop and I would say that I am having some pretty good results for a beginner in this aspect of photography BUT......
My HDR results in the main are in perfect focus with no evidence of camera shake. I generally use my camera (Canon 5D mk3) in LIve View mode and mounted on a heavy tripod. I set the camera to take three photos automatically +/- 3 stops to the mid exposure value of the scene.
My question / problem is that if I take a sun rise shot everything is in perfect focus but if the sun is in the frame, after applying the HDR process, the sun has a significant "ghost" up to a third of the size of the sun! Also any clouds immediately around the sun have a strange shape and a vivid orange color. Other features within the frame remain in perfect focus. In the individual frames there is no such ghost round the sun and the clouds look fine, all be it that two of the pictures are over / under exposed by intent. Why is this happening in HDR and can I stop it?
To anyone who may be able to help with this I would stress that shots without the sun in the frame are sharp and have no evidence of any ghost or similar defects.
My LR version is 5.7.1 and my operating system is Windows 7 pro

What version of PS CC 2014 are you using? There was an issue with a couple earlier versions some months ago where auto layer alignment was messed up. I remember it affecting focus stacking, but maybe it affected HDR creation as well.
Also, the first time I tried to work with your second set of images, using File / Automate / Merge to HDR Pro in Photoshop and selecting the individual files on disk, the alignment didn't work, either. Then I opened the three images in ACR and enabled lens corrections, clicked Done in ACR, then when I tried the Merge to HDR Pro a second time things were fine. The original CR2s had no ACR settings whatsoever and I don't have a D7000 to have enabled lens profile corrections by default, so no lens corrections were performed, originally, the time the alignment didn't work.
The current version is PS CC 2014.2.2 from Help / About Photoshop...
The metadata in the saved JPGs only says PS CC 2014, not the precise version.

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