There are a few reasons why custom fields don't show up, firstly, check if you've re-indexed after creating the new custom field. JIRA requires reindexing so it can be able to search through the fields.
Second, make sure the custom field has a Search template selected.
And thirdly, if the Customfield is only applicable for a certain project or certain bugs, be sure you've selected to only limit the search to those!
We have a full KB on this page.
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