To answer your question, nobody can give a 100% accurate answer. There's many possibilities, all of which require other questions asked. For a fact, something is causing 100%cpu usage. This can happen in several ways. You have something in your system, such as malware (not detectable by most Antivirus, they are different processes, you'll need malwarebytes for that) or you can have an nvidia driver issue, it'll be labeled pre-font cache and can easily soak upto 50% cpu usage (task manager, processes tab, all users) or it could boil down to you the user setting expectations of detail settings the gtx1060 is capable of, that the fx6300 is struggling at. Simple OC to @4.0GHz or better is the usual cure.
All of this can be dependent on the games in question. Skyrim, WoW, gta:V etc are very cpu dependent, more so with mods, and don't do well on fx Cpus since not only relying on core speed, but single thread performance, which fx Cpus suck at.
There's also issues with windows 10, some updates are creating havoc with some pc's, if you must, remove the last few updates, see if that affects anything, and reinstall if not.