FBI director James Comey values his independence from the White House and executive branch.  But increasingly, he is rubbing members of the Obama administration the wrong way, as he won't play ball on several important issues.  This is leading to a level of frustration with the bureau as the administration tries to play politics with law enforcement.

The Hill:

The FBI’s demand that Apple help unlock an iPhone used by one of the San Bernardino killers has outraged Silicon Valley, a significant source of political support for President Obama and Democrats.

Comey, meanwhile, has stirred tensions by linking rising violent crime rates to the Black Lives Matter movement’s focus on police violence and by warning about “gaps” in the screening process for Syrian refugees.

Then there’s the biggest issue of all: the FBI’s investigation into the private email server used by Hillary Clinton, Obama’s former secretary of State and the leading contender to win the Democratic presidential nomination.

A decision by the FBI to charge Clinton or her top aides for mishandling classified information would be a shock to the political system.

In these cases and more, Comey — a Republican who donated in 2012 to Mitt Romney — has proved he is “not attached to the strings of the White House,” said Ron Hosko, the former head of the FBI’s criminal investigative division and a critic of Obama’s law enforcement strategies.

Publicly, administration officials have not betrayed any worry about the Clinton probe. They have also downplayed any differences of opinion on Apple.

But former officials say the FBI’s moves are clearly ruffling feathers within the administration.

With regards to the Apple standoff, “It’s just not clear [Comey] is speaking for the administration,” said Richard Clarke, a former White House counterterrorism and cybersecurity chief. “We know there have been administration meetings on this for months. The proposal that Comey had made on encryption was rejected by the administration.”

Comey has a reputation for speaking truth to power, dating back to a dramatic confrontation in 2004 when he rushed to a hospital to stop the Bush White House from renewing a warrantless wiretapping program while Attorney General John Ashcroft was gravely ill. Comey was Ashcroft’s deputy at the time.

That showdown won Comey plaudits from both sides of the aisle and made him an attractive pick to lead the FBI. But now that he’s in charge of the agency, the president might be getting more than he bargained for.

Indeed he is.  Leaving the reservation on the Apple encryption issue is one thing.  But contradicting the president on Syrian refugees, as well as his suggestion that BLM rhetoric is leading to an increase in violent crime, angering the president's black base, could eventually make Comey a target. 

And what happens if Attorney General Loretta Lynch refuses to indict Hillary Clinton?

Hosko suggested that a showdown over potential criminal charges for Clinton could lead to a reprise of the famous 2004 hospital scene, when Comey threatened to resign. 

“He has that mantle,” Hosko said. “I think now there’s this expectation — I hope it’s a fair one — that he’ll do it again if he has to.”

There are hints that Comey and other high-ranking FBI officials will resign in protest if DoJ tries to drag out a review of FBI evidence in the email scandal past election day.  But Lynch has to get the evidence first, and there's no indication that the FBI is close to wrapping up its investigation. 

One thing is certain: Comey will not allow political interference in the FBI's decision on whether to prosecute Clinton or not.  He and tbe bureau will do their duty and let the political chips fall where they may.