Granting patents in the context of permissively licensed open source is a generous act and making the grant conditional is a way of not giving up your ability to form the strongest possible defense when you're brought into patent litigation. If you have been following along the recent years events (where is that patent apocalypse, anyone?) then it should be no surprise why companies need to do that.
Conditional patent grants are not new. Apache License v2.0 has a conditional patent grant [http://www.apache.org/licenses/LICENSE-2.0]. Google added a conditional patent grant to WebM, complementing its Modified BSD license [http://www.webmproject.org/license/additional/]. Google's Dart project is licensed under Modified BSD and has a.. you guessed it - conditional patent grant [https://code.google.com/p/dart/source/browse/trunk/dart/PATE...].