The daily reset doesn't happen until JP midnight / 0800 PDT / 0700 PST. They probably had two or more strikes from yesterday still.
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From my experience talking to a vendor or retainer when the duty pops dont cancel the duty. Yeah you gotta close a couple windows but you have plenty of time to accept the duty as for the penalty you have to miss "x" amount in a day to actually get a penalty. A one time miss doesnt penalize.
I just tested it on my end and wasn't able to get the same results.
First test was on an alliance raid, played around with my retainer, still remained in queue. Canceled the duty finder (with no pop) fine, no penalty applied.
Second test was on an expert roulette which popped instantly, went to talk to my retainer after the queue popped, the option to join remained (was just minimized to that little tab instead), and I had to manually withdraw which earned me a strike per the norm.
I'm really bad about rolling through my retainers to refresh Quick Exploration when those seconds are ticking down, so I can attest that doing that won't knock you out of the queue even when it's already popped. Withdrawing before it pops also won't give a penalty. So if the game is automatically cancelling your queue just for talking to your retainer, that's a bug and should be reported.
If you're letting the duty pop box go down to zero while you talk to your retainers and never accept it, that will get you a penalty.
The only time I've had an issue is when I've been in a cutscene when it pops, or occasionally zoning if the transition is a little laggy.
I dont think you should be oenalised for timing out the DF window for a few reasons, but I wouldnt say its a problem either.
I made post sort of on this other day with how UI works with menus, that I simply can't just use them all at same time, but I need to close a menu top open a menu or use a menu.
been bugging me from 1.0 but it is what it is when comes to menu limitations.
I think there should eventually still be a penalty as a deterrent to doing it too often, since it does affect those who accepted the duty. But maybe a three strike system before a penalty. That's 9 times missing the queue before someone gets locked out for the day and I'd say that's fair.