Updated Bulger photo/wbur

The FBI has gotten plenty pats on the back for capturing Boston mobster James “Whitey” Bulger, who had been on the run for 16 years and was a long-time snitch for the bureau.

But the capture has dredged up plenty of old wounds — the fact that the FBI protected Bulger while he acted as an informant. There have been allegations the FBI sabotaged cases of other agencies like the DEA to protect Bulger, who was eventually charged in 19 murders.

The Boston media has been relentless in questioning the resolve of the FBI to capture Bulger, suggesting the agency wanted to avoid what’s about to happen: A dredging up of allegations of old — and possibly new — that the agency had some crooked agents and did some highly questionable things.

Rep. Stephen Lynch (D-Mass.) wants the Justice Department to investigate how the FBI handled Bulger. He said maybe the Justice Department can glean new information to shed more light on the matter, according to the Boston Herald.

“There may be an opportunity to gain additional information regarding the FBI’s involvement in these crimes. It remains the responsibility of the Justice Department to see that a full investigation is completed,” Lynch said in a statement to the Herald. “With the capture of Mr. Bulger, my hope is that this (arrest) will bring some closure for the families of the victims.”

Boston FBI agent John “Zip” Connolly is behind bars for his handling of  Bulger.   Connolly was convicted of racketeering  in federal court and second-degree murder in state court in Florida for helping set up the 1982  killing of  World Jai Alai boss John Callahan in Miami.  Another ex-agent was implicated in the case but died in 2004, according to the Boston Herald.

Connolly , now 70, was accused of tipping off Bulger and Stephen Flemmi that Callahan was likely to implicate them in a murder. Hitman John Martorano killed Callahan in 1982.

The questioning of the FBI’s resolve in the case prompted Boston FBI Richard DesLauriers to issue a statement on Friday:

“Any claim that the FBI knew Mr. Bulger’s whereabouts prior to the FBI’s publicity efforts this week are completely unfounded. When we learned his location, he was arrested promptly.”

Some in the media haven’t really questioned DeLauriers’ resolve, or for that matter some of his  his predecessors, but they have raised questions as to others when Bulger first went on the lam in the mid-90s.

“It may be true that the new crop of agents and federal prosecutors are clean and wanted Whitey,” wrote Michelle McPhee in the Boston Herald .

“But there are too many unanswered questions about how he got away in the first place that should make U.S. Attorney Carmen Ortiz want to hand this case to an independent body, so the taint of the dirty Boston FBI office of the past does not leave a stench all over the work the feds are doing in this city now.”