Photoshop Elements 13 to Lightroom 5

I use Photoshop Elements 13 as well as the Nik collection as outside editing sources with Lightroom 5. All are recognized through “Edit In” in Lightroom, but only the changes made through the Nik Plugins directly show up in Lightroom once I hit save. In Elements I have to save my changes to the image and then re-import it into Lightroom. What am I doing wrong?

You should be editing and saving a copy out of PSE and in that copy the changes will be seen.  LR may be able to automatically import that copy as you save it if you are starting with a raw file in LR, but probably not if you're starting with a non-raw file.  If you are starting with a non-raw file (e.g. a JPG) then you should never save over the top of it in PSE because LR still needs to have the unchanged original that its settings apply to.
Without knowing a few more details about what types of files and what steps you're doing, it's hard to guess if another workflow might be better or if something is not working as expected on your computer, or if that's just the way things are.
The workflow that does work for me using Photoshop (not PSE which I don't have) is:
Import a raw file into LR.
Make adjustments in LR.
Use Edit in Photoshop from LR.
Make adjustments in PS and noting that the document title in PS uses a file extension the same as my raw file.
Do File / Save in PS.
Back in LR I see my original file with a raw-file extension and next to it and/or stacked with it the saved file as a TIF (or maybe PSD) that has just been imported into LR automatically from my Save in PS.

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