Post #32 suggests the OP has resolved the problem, or at least for now, with a change of the configuration of speaker sizes in the receiver's menus.
I'm going to make a suggestion based on what I have read so far.......Should the problem return, it might be useful to run your receiver in "Bypass" mode, which most AV receivers have a version of although it's called something different across brands (e.g. I think Yamaha calls it "Direct" while my Rotel calls it BYPASS). (Edit note* Yours calls it "Stream Direct") This circumvents all the digital circuits that might be causing the problem. MOST IMPORTANTLY, and this is the intended takeaway from this post, is that YOU WILL NOW BE LISTENING TO AN ANALOG SIGNAL STRAIGHT FROM YOUR CARTRIDGE>PHONO-PRE>PREAMP>POWER AMP>SPEAKERS!!!
Most, not all, choose to listen to records at least in part to experience analog sound without the signal being converted to digital and back to analog. When you are listening in the way you have described, the signal will be coming from your cartridge to the phono-pre. If you are using any of the processing tools your receiver offers, such as the large/small speaker menu you have spoken of, the signal is most likely routed through your receiver's digital circuitry in order to carry out those functions. This means the analog signal is converted to a digital signal after it leaves your phono-pre and will therefore sound like a digital signal upon completing its journey to your speakers.
If that is what you desire, then you are good as gold. If, instead, you wish to take advantage of what most consider a sonic benefit by keeping your signal analog straight through, you will need to put your receiver in the bypass mode, or whatever that is called on your particular make/model. Should you wish to compare the sound, and I highly suggest you do, between the two just switch back and forth between bypass and a digital mode, for example 5-channel stereo or whatever mode you had been running in. The difference, at least to my ears and in my case, is startling!
I'm just mentioning this here because for several years I was under the misconception that my preamp (Rotel RSP-1570) in 5 channel stereo was still in an analog mode.....NOT! 5-channel stereo is indeed a DSP (digital signal processing) mode and I finally figured it out through some experiments with subwoofer connections. WOW! What a difference it made!
I know this is a bit off-topic, but couldn't help commenting when I saw the likelihood that this was what you were doing and remembered my own delight upon making that discovery and subsequent changes to how I have things configured. Give it a try, and should your initial issue have been due to some glitch in the processing of the signal, you might also thereby have discovered a fix to that in bypassing it all.
Happy listening, amigo!
PS - Most of the home theater receivers I'm aware of will only send the (BYPASS-DIRECT) analog signal to your FRONT or MAIN speakers. Don't let that slow you down because if you get things set up correctly, you will never miss your center/rears (which will all still be available for digital sources). The fronts will produce a sound stage that will take you where you wanna be if you're sitting in the proper listening position and have your room modestly well-appointed. Should you have a subwoofer, you will NOT be able to use the typical connection because that goes back through your digital circuitry. You can remedy this, however, by connecting the sub/subs to a ZONE pre-out. This has the added advantage of being able, with your remote from your listening position, to control the volume level of the sub/subs without having to move out of the listening position.