At the very top of the chain of command for the federal police forces is the Department of Justice. The Border Patrol is just another box in a command chart of an alphabet soup of police and security agencies.
Last week, ‘….The Justice Department moved Friday to shield Attorney General Eric Holder from prosecution after the House voted to hold him in contempt of Congress….’ To be found in contempt of congress while shielding youself and your department from a botched operation (Fast and Furios) which resulted in the death of a border patrol agent could be construed as tampering with evidence for which there are a lot of people in prison. Justice Department shields Holder from prosecution after contempt vote
However, let an agent get caught in a smuggling operation and it is a ‘balls to the wall investigation.’ Ex-border agents accused of smuggling
It appears to be a matter of perspective and related to your position in the food chain.