gosh, there are certainly multiple accounts of what this issue is about...
Taken from the Slate.com article cited above:
"John Pike, who runs the invaluable globalsecurity.org Web site, told me what that cut was about : The Air Force's National Reconnaissance Office had appropriated that much money to operate a spy satellite that, as things turned out, it never launched. So the Senate passed an amendment rescinding the money—not to cancel a program, but to get a refund on a program that the NRO had canceled. Kerry voted for the amendment, as did a majority of his colleagues."
No mention of the headquarters or slush fund there... but the Washington Post is certainly a quotable source as well.
This article also references an amendment to the proposed bill that isn't listed in the congressional record.
Kerry submitted his proposal in late september, only four days after the news about this supposed broke in papers. Taking into account the work necessary in drafting legislation coupled with the very recent discovery of this potential mismanagement. This leads me to believe that the cuts proposed by Kerry were unaffected by this development. His remarks on the senate floor a year and a half later about the state of our intelligence budget solidifies that hypothesis.
So what are we to do about conflicting accounts from 3 sources (globalsecurity/slate, congressional records, washington post)?
i will take the congressional record, a document that makes no mention of amendments, no mention of specific overspending, no mention of the NRO and submitted within days of a seemingly related news story.
if kerry sought to single out the NRO for their poor spending, then i believe he would've noted that in his bill rather than making cuts to the general discretionary fund of the overall intelligence budget.
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addendum:
the slate article referenced the NRO as part of the Air Force's apparatus when in fact it is a separate entity... a peer of the AF's intelligence gathering organization.
http://www.intelligence.gov/1-members.shtml
when you check these things out... it is amazing what inconsistencies are found. wow...