Most military aircraft, and a fair few others, do not transmit their location and so most websites cannot plot them. Planeplotter is clever and uses a process called multilateration to 'find' and plot the non-location transmitting aircraft. This means that you do not miss the interesting aircraft like the KC135 (63-8040 RCH172) that has just gone over my house on the way to Europe.
However, the E6 does transmit its location and has done for the last few years. Why this occurs I do not know but it does make seeing it so much easier.
Andy S