Why does the select tool stop working and images save with areas missing?

I have been working on an image using simple tools (only select, crop and scale) and no more than 4 layers.
The quick selection tool, magic wand tool and polygonal lasso tools are not selecting simple areas. They leave square sections unselected, and eventually I can't select anything on my canvas. The paint tool also does not work. I decided to save the image I had made even though it was unfinished, and upon reopening the file (a PSD) there were square transparent areas that were not there when I saved it (see image)
This is what I've tried:
I work on the layer selected
I have reset all the tool settings back to the default ones
I have reset the program preferences back to default settings
The Photoshop CC software is up to date
I have turned the program and my computer on and off again
Can someone please help?

Is the damage actual or only display (are the layers complete according to their previews in the Layers Panel)?
Does turning off »Use Graphics Processor« in the Performance Preferences and restarting Photoshop have any bearing on the issue?
What have you done for trouble-shooting so far? (Restoring Preferences after making sure all customized presets like Actions, Patterns, Brushes etc. have been saved mis usually a good starting point):
http://blogs.adobe.com/crawlspace/2012/07/photoshop-basic-troubleshooting-steps-to-fix-mos t-issues.html

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