I don't exactly understand what I have to do to dig into this :(
But there is some information that I can give you:
step 1 - Zip64 archive was created (one entry)
WinRAR says "No errors found during test operation".

step 2 - first file was added to archive (two entries)
WinRAR says "No errors found during test operation".

step 3 - second file was added to archive (three entries) with exception "ICSharpCode.SharpZipLib.Zip.ZipException : End of extra data"
WinRAR says "C:\...\test_file_archive.zip: Unexpected end of archive" on open and "C:\...\test_file_archive.zip: The archive is corrupt" after test operation.
WinRAR 3.71 shows that "test_file_source.txt" file size in archive has become incorrect and "test_file_source2.txt" file is hidden.


But Total Commender 7.02a shows that "test_file_source.txt" file size in archive has become incorrect.

Sorry for large post with images. I hope it will help somebody to solve this annoying problem.