I am using the paid theme of Love Me Do. I have written them about this issue and they have said it could not be due to their theme programming as theirs does not touch the code that deals with wordpress galleries.
And yes I am using the native media gallery, no plugins or shortcodes. And when this problem began I only had one plugin installed that had to do with images – “Image Slider” which I can’t imagine would interfere with wordpress galleries or rearrange coding as they don’t overlap at all.
The problem seemed to of began after a wordpress update was released but I cannot remember which one as there have been so many in the past few months.