It is what is mentioned in this fragment of the article:

"When power flows into the EmDrive, the engine warms up. This also causes the fastening elements on the scale to warp, causing the scale to move to a new zero point"

Basically, thermal expansion of the thruster and the measurement device causes the rest position of the thrust balance to drift with time, which is hard to differentiate from the actual thrust generated. This is most critical when the thrust-to-weight ratio is low, as is the case here.