My theory is that the root of the problem is that there is a bug in the part of the receiver that handles overlaying the GUI and/or drawing the GUI where it can get confused to the point where only completely reseting the buggy part will fix the problem. Power cycling should work except that if you're enabled either the HDMI standby through or Network standby modes much of the receiver still gets power including the affected part. Pulling the plug on the receiver guarantees that this confused part gets reset back to a working state.
I strongly suspect what causes it to get confused is either a non-standard TV resolution or a standard TV resolution using non-standard TV timing. For a given standard TV resolution and refresh rate (eg. 1920x1080 60Hz progressive) there are at least two standardized sets of timings (CEA/EIA and VESA reduced blanking) and countless possible non-standard ones. The CEA/EIA timing are the ones standardized for the consumer electronic industry, and I assume are the only ones that these receivers officially support, while the VESA reduced blanking timings (CVT-RB) are ment for flat panel computer monitors that can handle shorter blanking intervals.
My guess is that earlier this year DirecTV tried to switch to using timings that weren't CEA/EIA compliant. Whatever they did affected a wide range of receivers, not just Yamaha's. It wouldn't have had much of a affect, if it all, on TVs connected to directly to DirecTV boxes because TVs are usually designed to handle a wide range of resolutions and timings, including those ment for computers. The likely reason DirecTV would've done this is to reduce overall the bandwith of the signal. For example, using CVT-RB timings instead of CEA timings reduce the pixel clock required to display 1080p60 video from 148.5MHz to 138.50MHz. Possibly DirecTV decided that they needed to reduce the bandwith because either their hardware or their customer's hardware (eg. cables) couldn't always be relied on to handle the higher bandwidths.
Anyways, this is all fairly speculative. All I know for sure is that unplugging the receiver for a while usually fixes overlay problems.