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If the default log file configuration of a DBO-schema geodatabase in SQL Server is modified to use pools of session-based log files, the pool of log file tables are not used, and new session-based log files are created in the individual user's schema.
This is a known issue in 9.3.
This issue was fixed in ArcSDE 9.3.1. Either upgrade the geodatabase or use the default session-based log file configuration. The settings for this are as follows: