I thought this question was dealt within a previous discussion, but it has been pointed out to me that it remains somewhat open. My impression was that if you say "er liebt sie immer noch" you were simply talking about a couple that had been in love for a very long time, whereas if you said "er liebt sie noch immer" there was an additional implication to the effect of "despite the way she treats him, he still loves her". Am I totally missing the nuance here?
First of all it is important to point out that we are talking about a nuance here. So AFAIK there is no written rule about it.
I think you're right with you're assumption that "noch immer" can have a slightly negative touch.
If a context or an opinion on the subject is given in the same sentence or a preceding one there is no difference between the two.
Obwohl es nötig wäre, regnet es noch immer nicht.
Obwohl es nötig wäre, regnet es immer noch nicht.
In this example the person wants it to rain (possibly because the ground is too dry), but it does not. So it is clear that the person hopes for a change, thus it "immer noch" and "noch immer" both have a negative nuance to it.
If the two are used in a sentence without much context, as could be the case in a conversation, the nuance can slightly differ. But IMHO only if you're talking about thing where you doubted it would stay the same, but you hoped for it (i.e. the sun shining, or somebody loving someone).
Die Sonne scheint immer noch.
Could be understood as "The sun is still shining, as I hoped". So the person is happy with the situation and maybe surprised it didn't change to the worse.
Die Sonne scheint noch immer.
This on the other hand could be understood as "The sun is still shining, although I hoped for rain/snow". In this case one is rather disappointed the situation did not change.
A better example would be love:
Er liebt sie immer noch.
Er liebt sie noch immer.
But if one is talking about something negative (i.e. bad weather), or it is clear that one is not happy with the current situation "immer noch" and "noch immer" don't have this different nuance.
Es regnet immer noch.
Es regnet noch immer.
Both imply that the person wanted the situation to change for the better.
In the end the important thing is what you would stress when speaking to tell if "noch immer" or "immer noch" express dissatisfaction or rather surprised agreement with a situation.
It may be that this varies in the different language regions. In Swiss german "immer noch" is commonly used, while "noch immer" is not that common. The two are emphasized differently as well (here in Switzerland):
Es regnet NOCH immer.
Es regnet IMMER noch.
So the local dialect may be a reason why for some people there is a nuance while other people don't see any.
There is no difference in semantics only in phonetics.
I have desire burning for you.
I have a burning desire for you.
Just a more elaborate way of saying things. Also sounds more old fashioned to say:
Er liebte sie immer noch. <-- past tense --> he still loved her
Er liebt sie noch immer. <-- present progressive --> he loves her - still (He has loved her and is still loving her).
Er liebt sie immer noch. <-- present fact --> he still loves her. (I just checked and yes, he still loves her).
I think "immer noch" has a tendency to "has not stopped", whereas "noch" sounds a bit like "still, but may change in future".
Ich arbeite noch. - "I am still working (although I am going to stop working soon)."
Ich arbeite immer noch. - "I am still working (since this morning)" / "I have not stopped working."
Therefore, you could say "Ich liebe dich immer noch" to loved one, but "Ich liebe dich noch" sounds a bit like a threat.