Is there any subtle difference?

"What....do...." asks what's the next step in whatever you happen to be doing. Oftentimes, Bot, the implication is that you might be stymied

...whereas "What...doing..." merely asks with what you're occupied at the moment

They have completely different meanings.

The difference is not subtle.

Not a bit

Just to reinforce what Beth has told you:

The phone rings:

Hello

Hey Bob, what are you doing right now?

Nothing . . . just watching teevee . . . why?

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The door opens and a man comes in to find a woman lying at the foot of the stairs, and his friend standing at the top of the stairs.

Bob! What happened?

She kept hitting me, and I just pushed her away from me. But she fell down the stairs.

Well . . . what do you do now?

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Not at all the same, and not at all subtle. "What do you do now" would almost always mean how one intends to deal with an unforeseen circumstance.