It looks like you are not comparing the same searches. The splunk-system-user account is used internally by Splunk to accomplish a lot of background work, so it is doing a lot of searches (and possibly alerts) that are more complex than most user searches.
Ad-hoc searches run by users, typically using the Splunk GUI, have a higher priority than background or scheduled searches. They are also typically less complex.
If this doesn't answer the question, then can you post a specific search that was run by both users, and give the execution time statistics for both searches?
... View more