The shuffle is playing the 1 and the 3 in a triplet. In others, if you are thinking xxx xxx xxx (123, 123, 123), which are triplets, just drop the middle one. This makes it x x, x x, x x (1pause3, 1pause3, 1pause3), etc.
Makes sense?
The upstroke is on the 3 of the triplet.
D pause U-D pause U-D pause U...