Unless they mean it humorously, when people utter this phrase – “but I’m not complaining” – they are *always* complaining; i.e., they are expressing “pain, grief, or discontent.” What these sad and/or irritated individuals mean to say is this: “But I’m not whining.” That is, they are not complaining in a petulant, feeble, long-lasting, or high-pitched manner. Nonetheless, they *are* whining, usually, despite their protests of innocence, aren’t they?
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To me the words “I’m not whining” don’t speak for themselves (them self?). Too many variables… the source, the subject, the body language, tone of voice, etc. I always try to draw a distinction between “critical perspective” and negativity, and other similar ideas.
A person could start a sentence “I’m not whining” and yet finish with a clear, unbiased observation or critique.
That said, most of the time, you’re right.
If the pitch of the voice saying “I’m not whining” is higher than normal, it’s whining.
basil.CA 
Really depends on context.
“Fred’s whining, but I’m not whining.”
They’re not whining.
But I agree that if they say,
“it makes me both sad and angry, like a starving inarticulate child, that Billy doesn’t want what I want out of our relationship, but I’m not whining”
Then they’re dumb as hell.