You need to create a new instance of Oracle on your DB machine for each install of Windchill. You can NOT share the DB instance between Windhills. I have done this in a test environment when I migrated from 9.1 to 10. I loaded the 9.1 data, which was in Oracle 10, into a new instance of Oracle 11 and then created another instance for the WC10 data. Exported from the 9.1, imported to the 10.0 and ran the schema update tool. All worked fine.
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