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There is no Time data type in Tableau, so the actual data fields are still date/time (even though they are formatted to only show time). Thus, comparisons will still look at the date component. If you want to compare only the times, then you'll need to edit the date/times to make sure the dates of both variables are the same. You can do that by creating a calculated field kind of like this:
MAKETIME(DATEPART('hour', ([Date])), DATEPART('hour', ([Date])), DATEPART('hour', ([Date])))This will create a date/time field with date component 12/30/1899.