Description:
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From the documentation:

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There are two special-case header calls. The first is a header that starts with the string "HTTP/" (case is not significant), which will be used to figure out the HTTP status code to send.
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and

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The optional replace  parameter indicates whether the header should replace a previous similar header, or add a second header of the same type. By default it will replace [...]
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But as can be seen below, header fails to replace headers in all cases.

Reproduce code:
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http://toolserver.org/~overlordq/results.txt

Actual result:
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As can be seen in the code linked above, header only truly replaces a similar header in the case if the Status is 200, for every other status code (that I've tested) PHP will output a duplicate header which does not conform to CGI spec.