Which GPS are you using? Is it USB or Serial?
USB units don't use the "follow map" feature, so your track won't be shown as it downloads. Can you see trackw when the "Save Tracks" dialog comes up after download?
When you say only hand drawn tracks are showing up, the only real difference between hand drawn and real tracks are that real tracks have time and elevation components. So, it could be that your gps tracks are being shaded by elevation or speed, making them hard to see on the map. Just an idea.
But when the save tracks dialog comes up, shading is turned off for those tracks, so they should be there.