Lightroom CC exports Jpgs in wrong orientation ONLY when Overwriting WITHOUT WARNING

This is the first time I post so please bare with me, I will try to explain as much as I can because it is an specific issue.
The computer I have at work uses Windows 7 pro (Brand New Computer). I import pictures from a network drive, manipulate the pictures and then save them to the same drive. When I see the pictures in the folder browser on windows the pictures have a landscape orientation (even though they should be portraits because they are head shots). Once I import those pictures to LR they appear with the right orientation (portrait), so I play with the pictures and export them to a JPG file. The issue I'm having is when I export with the setting "Overwrite WITHOUT WARNING", I see the picture in the file explorer (Windows) and I can see all the changes I made, but with the old picture's orientation (the wrong one, Landscape) . However, If I choose to create a new file (not overwriting) it will have the orientation I viewed in LR. (The correct one, portrait).  Anyone knows how to export overwriting with the orientation I was seeing in LR?
Thanks,
//UPDATE: Also, I just noticed cropping is NOT working when exporting with the same setting "Overwrite WITHOUT WARNING". I had to create new files on a folder and the move and replace in Windows File Browser.

Yes I have been trying to use my main catalogue, not the back ups - I thought the main catalogue was updated in synch with the latest back up - the reason you can fall back on a back up if all goes pear-shaped. .
I have managed to resolve the issue as follows:
I accessed an external hard drive (bootable back up of main computer) and the main Lightroom catalogue. Upon launching Lightroom it gave me the option to use the last saved back up Catalogue and as the default one. This workaround didn't work the same on my main computer as recent image imports and work done were missing.
I had to delete the main catalogue on my main computer and drag the one from the external back up HD to rectify the situation.
I have no idea why this has occurred as all I did on my main computer was delete 10 redundant back up folders after which Lightroom failed to launch citing one of the oldest back ups as missing.
I wonder why Lightroom saved the most recent back-up (upon closing Lightroom) in a Zip folder only? - not noticed this behaviour before.

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