>>In general it can be done, but it would overcomplicate the system.
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>How so? Instead of authenticating the rater against the author of the first message in a thread, you authenticate against the author of the message that was replied to.

Well, it is not just a technical issue. Let's see the possible scenario.

How does the reply "know" that there was another question posted in it? Sould there be the mechanism to mark the "reply" message also as the "question" message?

The person who starts the thread automatically gets the access to links "Mark this message as a help to this thread" and "Mark this message as an answer to this thread". If somebody else posts another question in his the reply, should it mean that he automatically gets access to these links? How? Or everybody has to have access to these links?

If the answer is posted somewhere else in this thread and you look at the thread map, how do you know is it the answer to the original question or to secondary question? Or just mark them all as "Help to this thread"?

Should the secondary question message to be marked too somehow? Should they have different color of marks/stars?

How do the other users/potential answer givers know that there was another (even related) question posted in the thread? Should they read all the messages just in case? It is clear that posting another question in the reply to the long thread reduces your chances for the answer.

I can offer several technical solutions to all these questions (as well as you). But the main question is Why? What for? What does it accomplish? Existing points system may be not ideal, but at least it is simple enough, and even with that not all the users bother to mark messages and many still do not know about this system.

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>>It seems more logical if the new question is posted in a separate thread.
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>That may be true. Except in this case, the question was on the same topic. If you start dividing things up into too many threads, continuity gets lost. In this case, if somebody wants to have the ability to rate a response, they are forced to start a new thread. This does not make sense.
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>As for what is logical, I still contend that rating a response should be in the context of the person asking the question, not the person who started the thread.

IMHO, as for what is logical, the logical choice should be to follow the "Proper Etiquette for posting", for example "Do not start another question in the same thread" http://www.levelextreme.com/Rule.asp#E8