One drawback about Break-In Mode is that it takes about 3 days to complete. That's because it goes through multiple charge / discharge cycles, measuring capacity upon each discharge. The extra cycles help form the batteries to fully maximize their capacity, a process which otherwise happens naturally over the first several use cycles. Doing it this way maximizes them from the start, does so in an optimal way, and measures the true capacity upon completion.
Refresh & Analyze does basically the same thing with less cycles, so it reaches completion much quicker, and is appropriate for occasional on-going maintenance. It also reports the true measured capacity. As long as the batteries remain in regular use you shouldn't need to use Break-In Mode for occasional on-going maintenance, but if they have been sitting for many months unused or have otherwise become suspect, it's the most appropriate choice.
Discharge Mode also reports true capacity, but will not charge the battery first (making it not particularly useful to me). The other charge modes display charger output mAh upon completion - basically the amount of juice the battery took to charge, which dos not reflect the total capacity of the battery. Total capacity can only be determined via a measured discharge cycle.
And for anyone comparing chargers, AFAIK the Lacrosse BC700 offers equivalent Break-In, Refresh & Analyze, and Charge modes.