Make sure there is enough room on the mem card for the saves, also check you got the latest update from the 20th December.
Here's a ready made 3in1 OS setup for the ds1 (sdhc model only) attatched below with all the latest updates installed.
Another tip if using a large mem card of 4gb+ is to use the 'panasonic sd formatting' tool as the windows one sets the cluster size badly apparently, set the options in the panasonic format tool to , 'full format' and 'special formatting' set to on for best performance.
hxxp://www.2shared.com/file/4529581/31b7ee18/3in1_OS.html
Hold X or Y on bootup for DSTT/Y's menu or just run the apropriate .nds file to switch from one OS to another.