I took a more in depth look at what was going on with the various types of Hebrew dots, which I will separate into three categories. 1)puncta extraordinaria, 2) The dots in Koen Gh's example, 3) the dots in bi3mw's example.
1) Puncta extraordinaria: A feature of the Masoretic tradition, these actually appear to be related to very specific words.
They appear
exclusively over words and nowhere else. The obvious reason for this is so that they cannot be confused with the diacritical marks indicating vowels. They appear over only 15 words in the Hebrew Bible (listed You are not allowed to view links.
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Login to view. p.32). According to the authority on the subject, Paul de Lagarde (1863), all the manuscripts which feature them belong to this masoretic tradition and they are all copied from one archetype (see You are not allowed to view links.
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2) Koen Gh's example (Geneva CL 145, You are not allowed to view links.
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Login to view.). Let's look at this in the wider context of the whole page, which really helps elucidate what we are looking at. The page features large Hebrew letters. The feature Koen Gh noted is near a large, ornate version of the letter Chet. Underneath the Chet there are two diacritical vowel markers. These are known as
tseirei, and they indicate the sound short/medium "eh", like in "egg". So this tells us to pronounce the large letter as "Che".
Next to each large letter on the page, there is a small text, and each time, above it, there is a row of four small circles, sometimes blank, sometimes filled in. The small circles in each row feature diacritical vowel markers. In the case of the small circles near the Chet, the circles are each marked by three diagonal dots underneath them. These are
kubbutz, and indicate the long "oo" sound, as in "blue".
Why the small circles? According to the wikipedia entry on Hebrew diacritics, such circles are used to stand for "whatever hebrew letter is used" : in other words, they are used when it is the diacritical vowel markers themselves that are the focal point. In this sense, diacritical markers related to a small circle like this indicate a pure vowel sound. In the example above the text near the large Chet, the small circle with three diagonal dots (
kubbutz) under it conveys a pure "oo" sound. They are not puncta extraordinaria. They may be related to the small text beneath them in other ways.
For this reason, now that I have viewed this symbol in the broader context of the CL 145 page, I don't believe it is related to what we see in 116v, in spite of very tempting visual similarities.
3) I have yet to read more about the type of dots in Add MS 15299 offered by bi3mw, but will update when/if I do find something.