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I did start to notice this though when I began updating Decky more frequently. I thought there was one update in particular that broke it because my Deck wouldn't fully boot after it installed. This just occurred to me, and I'm only speculating, but maybe it doesn't like updating while docked. I only say this because I have installed updates to Decky and SteamOS in the past closer to when the OP posted and had no issues. I have had my JSAUX dock for a while now too, but really didn't use it much until the last 2 weeks. Within these last two weeks, I haven't added too many new plugins to Decky (I think the only one was "Backboard" (I don't believe it's the culprit; it hasn't gotten any new updates in the last 4 months)). I believe the issue occurred for the first time when I updated Decky while docked.
Maybe it or one of it's plugins has some sort of expectation from the display and waits for that before finishing bootup. I think it's more likely Decky because *most* of the plugins in the marketplace don't require root and afaik cannot control the bootup process.
Settings > Display, then tick "Automatically Set Resolution" to on. It seems the boot screen freeze only happens at 4K resolutions and by setting it automatically, you'll still be able to achieve 4K in-game, but you won't be locking yourself at the boot screen because it's trying to render the main menu at that resolution. This, unfortunately, comes at the tradeoff of your Steam Deck UI being locked to 1080p.
I'll give it a try, but I don't actually have any 4K displays lol. The projector I connect to is 1080p.
EDIT:
I don't have that option. My Display settings go from "Brightness" to "Night Mode" to "Dim" and "Sleep" to "Advanced". The only option in Advanced is "External display safe mode". I actually did come across this as a potential solution from some other post, but when I enable it, stay set. (It may have something to do with my projector having limited resolution output modes). If I am missing the setting you are referring to, maybe it's a difference in version? I'm on Stable for both OS and Steam Client.
(BTW, yes, those options only appear when you are docked)
TL;DR: External storage devices.
It's not the varying display settings throwing off the boot up process. It's storage.
I forgot that the reason that i really started using my JSAUX dock more was not necessarily to play on a bigger screen, but to expand my library even further with those super massive, controller only type of games (NBA 2K23 in my case). I ended up putting these games on another micro SD card that *could* be inserted into the Steam Deck's slot, but instead i opt for an micro SD adapter that's got both USB C and A (super cool product).
That adapter always stays plugged into my dock when I'm home, and when traveling, i put it on a lanyard. I already recognized that the constant mounting and dismounting of this drive can get a little wonky. I'm my limited testing, i found that when I'm docked and SteamOS isn't seeing those games on the card, i simply fully restart the deck (sometimes have to go into desktop mode briefly). Ultimately, the steam deck should be powered off when docking.
What i just found out moments before typing this is that instead of it being my dock that fixes my boot loop, it's that micro SD card. I just plugged that adapter directly into the deck, rebooted once more, and it was good to go. Furthermore, as long as it stayed attached, switching between SteamOS and desktop mode was as smooth as if i didn't have any external storage.
I really hope this helps!
To anyone out there who depends on having an SD card placed inside their Steam Deck, you may want to use the Automatically Set Resolution workaround.