When running the Apache JDO "TCK", JPOX needs to query the columns for a particular schema, and so uses DatabaseMetaData.getColumns(null, schemaName, null, null). This takes the order of 3 minutes on a dual-core Pentium 3GHz (with large ram). I've cut the JPOX part down to a stand-alone test (will attach it).
Thing to note is that with only the schema files d_* installed it takes the order of 20secs. When the schema_* files are also installed then performance goes downhill fast (even though they are in different schemas ... all *.sql file represents a different schema). No point in me postulating what could be the issue since you guys are the Derby experts.