If a person has failed a polygraph for one intelligence organization (the FBI), is he/she doomed to automatically fail the test from another organization? In other words, are the two agencies swapping polygraph records or other documents?

Phlyfisher,

If a person has failed a polygraph with any Federal Agency, i.e., FBI, CIA, NSA, DEA, etc., whether an intelligence specific agency or not, will surface if a NAC "National Agency Check" is conducted. 

A NAC will show if you have a file with any of the multiple Federal Agencies, and without question will disclose any previous polygraph exam regardless if one passed or failed. That said, the odds of you not disclosing a previous failed polygraph, and the results not being discovered is very slim odds. 

I can't speak for any other Federal Agency, however, I can speak to the FBI. If applying for employment with the bureau, a Local Area Check and National Agency Check will be conducted prior to scheduling a pre-employment polygraph exam. 

If any adverse information surfaces during the NAC, the issue will be evaluated prior to the polygraph. Depending on the nature and severity of the information, it may be determined to allow you to proceed. Likewise, the bureau may simply interpret the information to be not within acceptable parameters IAW the guidelines for employment. If this is the case, the process will be terminated.

Note: 
I know of a couple of current bureau employees that disclosed previous minor offenses (several years prior to applying with the bureau) to include an assault charge at a night club, and another for using marijuana. Both got in and are currently employed with the bureau. Point being, not all adverse automatically is considered to be disqualifying in nature. 

Good luck.

triple x