The form that is presented to select a quality/format has two dropdowns on the bottom of it, one or both will be set to prompt. Change these to the format and quality you want. Provided a stream with that format is available then it will download automatically at the quality selected. Otherwise you will be prompted. They are also available via Settings > Internet Downloads.
I am not sure what would be causing the refresh you are experiencing. The list views does not refresh as you describe upteen times per second. There is probably some conflict with other apps running on your machine. I know you do screen recording, this can cause flickering on some screens depending on how it is implemented and what is being screen recorded.
Hope you are feeling better.
JMR will pickup what ever protocol/format that sight is streaming and capture that. There is no way for you to change what the site is streaming unless they give you that option in their video player (or you control the site).
Some sites do stream different protocols/formats depending upon the browser you use. For example some sites I have seen stream rtmp/flv when using IE and hls/mp4 when using chrome.
For me, using chrome starrranch.org/blog streams hls/mp4.
Once the stream is captured, you can then convert it to any format/quality using the built in converter.
The muxing of rtmp/flv streams (which I am assuming is the muxing you are talking about) can be controlled by Settings > Internet Downloads > Advanced > RTMP. Auto fix and Rebase to 0 are the processes that are happening when Muxing is happening at the completion of an RTMP stream capture. Bot these settings make it easier to play back flv files in players. But they can be switched off if you dont want them on.
Months ago my posts re downloading YouTube live streams via URL were abandoned but I've revisited the problem and got a live stream going, this one - https://www.youtube.com/watch?v=6a3U8ButYsY
The huge problem is, I cannot have it automatically restart after a drop-out because Jaksta wants me to choose the "quality" to download - and it can sit there waiting while I am oblivious to it because I can't see the popup (even if I were in the room, which I may ot be). I can't see how to tell Jaksta to select the same quality each time, so that it can look after itself.
(Incidentally, another huge problem that I'd never seen before the past week or two is the Jaksta interface refreshing itself umpteen times per second, truly eye-watering. Am about to reinstall on top of itself first, if that doesn't fix it I'll have to do an uninstall/reinstall.)