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Drupal has a problem when clean urls are enabled.
Because mod_rewrite decodes the url query, anything in the query needs to be double encoded. The old code, and the code in the CVS patch you showed, only double encodes '%2f', '%26' and '%23' (most commonly used in URLs). However, it should double encode ALL %.
This problem can be seen with an attached file with a '+' in the name (eg, an attachment called 'apples+oranges.png'). This turns into '%2b' but the percent sign is not double encoded like it should be, and the link is broken with clean urls enabled.
This is corrected by the attached patch.
PASSED: [[SimpleTest]]: [MySQL] 190 pass(es). View
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch file_create_url-D6-1.patch. View
PASSED: [[SimpleTest]]: [MySQL] 17,421 pass(es). View
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch file_create_url-60.patch. View
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch file_create_url-59.patch. View