Refer to the first point in the "Troubleshooting" section at
Why can't I find the field I want to choose as a criterion? Some fields are only valid for a particular project/issue type context(see Configuring Fields and Screens for details). For these fields, you must select the project/issue type that the field is applicable to. Otherwise, the field will not be available for selection (even if you set the Project and Issue Type set to 'All'). In the example below, the 'Customer account' field is only available in the 'Angry Nerds' project.
So select the project, the particular issue type and you should be able to see the custom field. It also helps if you click "Refresh" (not the browser refresh) but the "Refresh" button available in the basic search.
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