It very infrequently means 'not okay' or 'I'm secretly having a bad day' or 'something is wrong, but I'm trying to hide/ignore it'.
"Hey, man, how are you doing?"
"I'm all right."
"Hey, do you want to go get some ice cream and play some Sega Genesis games?"
"That sounds all right to me, my friend."
"How's it going?"
"Just all right?"
Here, it implies the first speaker used 'all right' in an incorrect sense, which is not likely the case.
Which may be followed by:
"Not 'great' or 'spectacular'?"
This response assumes the day has to be extraordinary or noteworthy. It implies the second speaker feels it's up to them to spice up the first speaker's life, wants to rope them into some time-wasting activity, or just has a terrible sense of humor.