This issue is fixed in the latest version of the Network Link Conditioner - it's in the "Additional Tools for Xcode 8.1" download from https://developer.apple.com/download/more/.
I've tested all the built-in profiles and they work as expected.
If you installed link conditioner for previous Xcode version it will not work with Xcode 8. You can download Additional_Tools_for_Xcode_8.2.dmg from http://developer.apple.com/download/more/
then you will need to move the old link conditioner before installing the new one. Like this:
Install NLC from the downloaded bundle and try it out. (http://www.netmeter.eu can help you testing your network speed)
In my case I was using OS X El Capitan Version 10.11.6 . The NLC from the newest bundle "Additional Tools for Xcode 8.2" did not work for me. But NLC from "Additional Tools for Xcode 7.3" works like a charm. Reinstalling or changng Xcode is not necessary.