In ATK2008.10 there is a command called current, it makes a separate transmission spectrum calculation which is used to calculate the current.
For a finite temperature the current depends on exactly how much of the transmission spectrum is used, in particular for systems with a gap like graphene this method is not accurate enough.
In ATK11.2 the currents is calculated directly from the transmission spectrum, thus, you dont need an extra transmission spectrum calculation, you have control over which transmission spectrum is used for the current calculation and you can calculate it for different temperatures without any overhead.
Thus, it would be best for you to upgrade to ATK11.2 to perform the calculation, and you need more k-points, the transmission spectrum should look like a wedge, i.e. rise linearly from the fermi level.