You do have a 3in1 cart in the GBA slot, right? The 3in1 tool is for use with a 3in1 cart that plugs into slot2.
Assuming you do have a 3in1 cart plugged in.......try plugging in and unplugging the 3in1 a few times to sort of scrub the contacts between the cart and the DS. It's sounds like you are having a contact issue.