During the 17th century, musical notation underwent a fairly fundamental change. Bar lines appeared, the form of the time signatures and the notation generally took on a "more modern" appearance.

The changes were more than just superficial. While the way in which pitches were notated did not really change very much, the indication of tempo/time signature did and the change reflected a change in the way in which the tempo and the time signatures were viewed. There is actually quite a good article on Mensural Notation, the style of notation used up to about 1600 here, in Wikipedia

The sections on "Modes and Mensuration Signs" and "Proportion and Coloration" are of particular interest here. On the basis of the following;

Meters could be shifted in the course of a piece, either by inserting a new mensuration sign, or by using numeric proportions. A "3" indicates that all notes will be reduced to one-third of their value; a "2" indicates double tempo; a fraction "3/2" indicates three in the time of two, etc. The proportion "2" could also be expressed by a vertical stroke through the mensuration sign (the root of the modern "alla breve" signature).

It seems likely that Anglo's suggestion is correct. It is also possible that the 3/9 was not an error but deliberate (see the comment on 3/2 above), especially as the notation in the links above shows what would almost certainly be considered at that time as old fashioned notation.

Jeremy Barlow, in his introduction to his "Complete Country Dance Tunes from Playford" has a discussion on the forms of time signature and these were steadily modified in successive editions. Incidentally, Barlow has modernised all the time signatures in his book, especially where they might be unfamiliar.

Geoff