For submissions, "vouch" appears for submissions that are marked "[dead]", not "[flagged]". Same for comments, AIUI. Some confusion is understandable due to the fact they're usually correlated and the looseness with which "flag" is often used to mean either.

Good explanation. I guess the problem is that when posts are flagged, they seem to drop precipitously in the ranking, and there’s apparently nothing that can be done to vouch until the post is marked dead. But if flagging is tantamount to killing in terms of visibility, then the cure comes too late.