However, it turns out that this may not have been the precise reason for 39. So, why 39? There are two components to the answer. (1) First, a scourge with 3 thongs applied 13 times gives 39, and so Paul (and Jesus) may have suffered lashes from a scourge which would explain why they suffered 39 lashes.
In what I've read, secondly (2), the cutoff point in Jewish law was actually 40, not 39. So adding these two points together is one reason why 39 was used, because the next set of lashes with a scourge would give you 42. But under this assumption, Jesus could have been given 40 if a rod or other instrument was used.
At any rate, there are several rationale given for making the maximum at 40, according to different versions of the Bible:
- Punishing an Isrealite with over 40 lashes would cause the punisher to be publicly humiliated ("your brother [the punisher] will be degraded in your eyes")
- In some cases, a bit worse than the above: "thy brother will become despicable in thine eyes"
According, however, to written Jewish law, apparently they capped it at 39 because 40 was considered "full judgment" delivered by God, according to passages from Genesis and Numbers (and other references to 40 in the Old Testament). The 40 in Genesis, for example, refers to the 40 days and 40 nights of flooding. In Numbers, it refers to God punishing those who sinned by making their children serve as Shephards for 40 years. So accordingly, one might think that 40 was actually considered a death sentence, or at the very least, was considered entirely unthinkable as a punishment carried out by anyone other than God.
This seems to be the most plausible reading of the issue. Here is the source used for some of this discussion: http://bible.cc/2_corinthians/11-24.htm.