I think the difference is simple. The IRS and DoJ have no problem lying to Congress, because they have shown they are toothless tigers. They have held Holder and Lerner in contempt, and nothing has happened to them. So there is nothing to fear from obstructing Congress and even committing perjury if there is no one to prosecute the violations.
On the other hand, the judge in the Judicial Watch case ordered the IRS and DoJ to provide an individual to swear under oath as to the facts concerning these e-mails. If this person lied to the judge, the judge could toss him into jail immediately - no need to get the DoJ to prosecute. How many people at the DoJ or IRS are going to go to jail to protect the likes of Lois Lerner?
I know....They searched the “catastrophe” back up systems, only to discover that they too were “scratched”.