Have a look at;
http://www.splunk.com/wiki/Community:PerformanceTroubleshooting
It sounds to me like you are encountering some performance issues with your install (although there may be something else going on).
If there was any information you gather using that link that you wanted to paste here to help troubleshoot then feel free to do so (being mindful of any sensitive information).
For some additional info,
are these realtime/run-once/scheduled
searches?
Have you customized your install? E.g. do you use the default index or have you configured your own?
Is it just the single indexer for event log data or is it a main server for other forwarders/indexers, if so what sort of setup do you have?
Have a look through your jobs window in the top right to see if there are many jobs that are still running and see if their memory usage and time to complete seems excessive.
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