Ah, explanation is in the HJK review:

*[Repair LiIon & NiMH:
Repair runs 3 charges and 3 discharges, this means batteries ends up discharged. This mode do not allow selection of current.]*

So, it just cycles the batteries. IMO, +this function is worthless on Lion+, and may have some utility on neglected, abused, or stored NiMh.
I'm in the process of doing that with some stored NiMh right now. Run 'em down, charge, repeat, until the capacity stabilizes. May take 3-5 rounds to get to that point. Time consuming.
On older batteries that do not terminate well the automatic cycle/repair may not work very well. I think a more accurate word would be 'exercise' the battery, as it really does not 'repair' anything.