A couple of years ago we asked Kitware (developer and maintainer of metaimage file format) about Anatomical Orientation tag and they responded that it is informational only and it should not be used for updating direction cosines. We updated Slicer accordingly.
Interestingly, recently Kitware has revised this decision and now considering using AnatomicalOrientation tag to update axis directions after all. If Kitware ends up updating MetaIO library and mha reader/writer in ITK then Slicer’s behavior maybe become more similar to the Slicer3.
All these of course for your information only. To make your scenes usable in current Slicer, you need to follow @pieper’s recommendation above and fix up the header or apply a transform to your images as needed.