I've seen this same question come up a couple times, and my solution is different, so thought I'd share on a few of these in case others have the same problem I did.
The problem was that the query in my Alert was "search index=myindex sourcetype=waf httpstatus=400".
As soon as I removed the keyword "search" from the beginning of this query in the alert, it produced results consistent with manually issuing the search (index=myindex sourcetype=waf httpstatus=400). The rationale behind this (if I understood the support engineer correctly) is that the Alert passes the query to the CLI (i.e. /bin/splunk search ), so the CLI interprets the "search" item in my query as a searchable word, not a function.
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