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Sorry I am not offering a solution!
I am getting the same error trying to clip simple rectanlges with a buffer i generated. it worked just fine yesterday doing the same exact process with just a different Input Feature.
I've checked geometry, they are both feature classes from the same database.
I'm running ESRi 10.0 Build 4400 service pack 5
on Windows 7
ESRI please respond!!!
I exported all the files from feature classes to shape-files and saved it a folder outside of the databse. This worked just fine.
So Corrupted database?