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The EZ tolerance stack up table displays a message "calculated results are ignoring potentially significant 3D effects" and the RSS value is wrong when the hole and pin with clearance features involves in the 3D model for stack analysis.
From "Help Center" - "Creo EZ Tolerance Analysis" - "Common Error and Warning Messages": https://support.ptc.com/help/creo/creo_pma/r9.0/usascii/index.html#page/model_analysis/eztol/common_error_and_warning.html
I did see the pointed hyperlink but didn't get the exact cause, it seems the issue happen when 3D model involves the assembly feature for pin and hole with clearance, see attached image