This problem only appeared when I updated to the 2.085 release from the last 1.xxx release.
This happens when a new set of TV shows is added and then you scan for new content. With some (but not all ) seasons the .nfo files are created with the correct file names, but the content is identical to that created for the 1st episode of the season. For example xxxtvshow S04E05 has content which says it is S04E01, but it correctly calls the file XXXtvshow S04E05.nfo
Please let me know what additional you need to identify the problem.