That sounds stange. I never use the raft feature, no matter of platstic, (ABS, PLA, Ninjaflex, Nylon, Pet).

If the temperature and print speed is the same for raft/no raft and the buildplate is level the only factor left I can think of is the 0 height calibration.

Do you subtract the thickness of the paper (0,1 mm for normal 80g/m^2 printer paper) after you have calibrated?
The raft layer often use a higher layer height and width to acceive a better adhesion to unlevel beds.

Could that be one factor?