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Hi Robes

With your detailed explanation of the symptoms you experience I may have a possible answer for what is going on.

When you have a Smart Ojbect opened in PS, a copy of the original Raw file is placed in PS.  This is because when you save a PSD or TIFF, the raw file is also embedded in that PSD/TIFF file.  Any editing you do once the raw is embedded in PS will only affect the embedded file and not the original Raw file.

In CC and beyond you can link files into PS instead of just embed yet that is for another topic.

Hope this helps.