Ermy,
There are two possibilities:
1) Your attenuator was outside the normal range when it was adjusted. In this case, the amplitudes would read correctly at all reference levels, but the noise floor would come up a few extra dB at certain reference levels.
2) Your attenuator has been slightly damaged (typically from ESD), and only reads correctly at certain reference levels.
This is something we could repair if you are interested.
A good way to manually check your device is to inject a known signal, at -45 dBm or so. Check the reading at -40 dBm reference level, 200 kHz span, and then step the reference level in 5 dB steps up to 0 dBm. If any reading differs by more than 2 dB, your attenuator is probably damaged.