The problem is more than likely Anynet+. Anynet+ is Samsung's version of CEC (Consumer Electronic Control). The idea of CEC is to use your HDMI cable to control all of your devices that are connected via HDMI. The problem is that with the current HDMI 1.4 specs, not all of the CEC protocols are mandatory. In other words, the various mfrs have the options to enable or disable protocols as they see fit which results in incompatibilities with different devices. That will go away with HDMI 2.0 because all HDMI 2.0 devices will have to enable all of the CEC protocols (CEC Extended). There are no updates or upgrades that I know of for CEC. The easiest workaround is to disable CEC on all of your devices and use a programmable remote such as a Harmony.
All of your devices should be connected to your receiver with a single HDMI cable going to your tv. If you are using ARC (Audio Return Channel), I'd suggest disabling that and connect an optical cable from your tv to the receiver. That way, when ever you use the internal ATSC tuner of the tv, or use any SmartApps, the audio will be sent from the tv, via optical, to the receiver. Keep the tv speakers off. All of your other devices will send their audio to the receiver with just the video being sent to the tv. The ONLY advantage of ARC is that it eliminates the use of an optical cable. Both connection methods, ARC and optical, can only pass discrete 5.1 audio. If you connect other devices directly to the tv, quite often the tv can't, or won't, send any other audio formats other than stereo. Some tv's will allow what ever audio is presented to it via HDMI and pass that thru but I don't know about your particular Samsung. Most don't.
You will have to switch inputs following the above scenario but with a programmable remote like a Harmony, it's easy. I don't use ARC/CEC and just rely on my Harmony.