Gary Schenkel had been under fire from Capitol Hill after a series of reports uncovered security gaps at federal buildings.
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Republicans have lost three straight special congressional elections in swing districts.
While officials say the intelligence chief needs proper authority, they agree there's no appetite on Capitol Hill to pass legislative fixes.
One amendment would provide funding to hire more personnel and make improvements inside federal agencies that work on border security issues.
Full Senate unanimously approves legislation which would create more robust programs at agencies.
IG report also highlights drug use and sharing of pornography on work computers.
Poll says only 31 percent see Obama doing an excellent or good job dealing with the Gulf of Mexico disaster.
Agencies spend $60 billion annually on multiple award and enterprisewide contracts that often are duplicative.
Adm. Robert Papp Jr. takes the helm of the service; former commandant Adm. Thad Allen heads to the Gulf.
Whatever Dennis Blair's personal problems as director of national intelligence, the role is inherently awkward.