I have messaged Mike on a couple of occasions this year about that fact. Back in December he told me that the present values were lower due to the different setups between real time and trad leagues. He also said that the values would be adjusted once the real time leagues were finished for the season. Of course that did not happen. I just e-mailed him last week about it and he said that they would not be adjusted until the INJ bug was fixed.
I guess that this is only a one year problem and the teams that are really strong luck out this year. In years past before the drafts the PB values would be updated which not only changed PB values but the also the INN status of various players.