Jing, I think I have an explanation for why advanced search in the LTER skin would be faster at metacat.lternet.edu than at knb.ecoinformatics.org. The key is the indexPaths property in the build.properties file. I have fine-tuned the indexPaths setting at LTER such that all EML fields searched by the advanced search code are included in the indexPaths list. When this is not the case, the advanced search does perform extremely slow (as you are seeing at knb).
Below is the setting that we are using at LTER. If you cross-reference the values used in metacat.lternet.edu with those at knb.ecoinformatics.org, you will probably find a number of fields that were added to the LTER setting (and perhaps some fields that are used in KNB but not at LTER).
indexPaths=@packageId,@system,abstract/para,abstract/section/para,alternativeTimeScale/timeScaleName,associatedParty/individualName/givenName,associatedParty/individualName/surName,associatedParty/organizationName,creator/individualName/givenName,creator/individualName/surName,creator/organizationName,dataset/abstract/para,dataset/abstract/section/para,dataset/access/allow/principal,dataset/creator/individualName/givenName,dataset/creator/individualName/surName,dataset/dataTable/physical/distribution/online/url,dataset/spatialRaster/physical/distribution/online/url,dataset/title,eastbc,eastBoundingCoordinate,EcogridRegEntry/description,EcogridRegEntry/endPoint,EcogridRegEntry/serviceName,entityName,geographicCoverage/boundingCoordinates/eastBoundingCoordinate,geographicCoverage/boundingCoordinates/northBoundingCoordinate,geographicCoverage/boundingCoordinates/southBoundingCoordinate,geographicCoverage/boundingCoordinates/westBoundingCoordinate,geographicDescription,givenName,keyword,northbc,organizationName,originator/individualName/givenName,originator/individualName/surName,originator/organizationName,southbc,surName,taxonRankValue,westbc