I am carrying three batteries with me at all times for my D100. It is a bit of overkill, since the charge lasts for several hundred images. My batteries go down faster than advertised due to my choice of media. I use the IBM Microdrive (one gig) with its spinning platter, so I only get about 400 shots out of my battery.
You mention doing a "refresh" cycle on your batteries. I only have the charger that came with my D100, and it seems to charge the battery, not refresh by a deep cycle discharge and then recharge. What charger are you using that allows you to refresh and charge your batteries?