You should not use index-time extractions unless you have a very good reason for doing so and really know what you're doing. Index-time extractions affect performance negatively. You should always use search-time extractions unless there's a specific reason for not doing so.
This blog post covers the problem you might be running into: http://blogs.splunk.com/2011/10/07/cannot-search-based-on-an-extracted-field/
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