It might be because the storage in 9.3 Geodatabase is Low Precision.
I tried the tool, it worked fine for ArcGIS Desktop 10 and ArcSDE 10.1, but when i tried to run it on ArcGIS Desktop 10 and ArcSDE 9.3. It failed with below error.Please advise"An error appearsThe index passed was not within the valid range"
try rebuilding/analyze the indexes for the layers the error complained about.
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