After leaving my DS unused for over a year, I had the same problem - on plugging in the charger, the red charging light flashed on for about a second.
The problem is that Li-ion batteries have management electronics built in to prevent the cells from over discharging, but if they do get very low, the controller effectively open circuits the battery.
The DS charger sees no battery present and gives up after about a second (the red light goes out).
The trick is to get some charge into the battery so that the management electronics reconnects.
I managed this by using a 1K resistor. I fitted the battery with one resistor wire trapped between each battery terminal and its DS connection (so that the battery is connected as normal, but with the resistor across the terminals).
When I connected the charger, this time the red light stayed on. I left it for about an hour then pulled out the resistor. It continued to charge, and after a full charging cycle, it seems to work as normal.
Hope this help but be a little careful. Li-ion batteries tend to explode if mis-treated and if you short the DS battery connections, you will probably blow an internal fuse.
Jim, March 2010