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.