Clicking Run tells VSys to compare all of your non-archived, non-placeholder people against the exclusions file.
For each potential match it assigns a "score" based on similarity of name, DOB, zip code and state.
The filter VSys uses is relatively "loose", meaning that it will err on the safe side and suggest matches that could be but aren't likely rather than ignoring what might be real matches.
If you've previously told VSys that the person in VSys and the excluded person are not the same, and the excluded person's data (any) has not changed, and the VSys person's data has not changed (name, DOB, addresses), then VSys will not suggest that the two are a match. (If either the VSys or excluded person have changed and VSys sees them as similar, it will show the two as a suggested match again.)