Reuploading a file saves the file under the source name, not under the name of the already existing file.
It appears that the problem is the disabled wpDestFile field. Apparently at least Firefox 3.0.5 does not send that disabled field upon submit, and SpecialUpload.php thus reverts to using the source name instead (lines 403-407 in r46444).
Enabling the wpDestFile field just before submitting cured the problem in my tests.
Test case: go to [[File:Albert_Einstein_by_Suse_Byk.png]] at the English Wikipedia. Click the "Upload new version of this file" link. Choose as the source file a file named HCC.png from your local disk. Enter "Foo" as the upload comment. Click "Upload". You'll end up uploading [[File:HCC.png]].
Version: unspecified
Severity: major