Why I'm getting MD5 Sums don't match! error?
Once the file has been uploaded, S3 computes the MD5 hash of the data. s3cmd computes the MD5 hash of the local file, and compares it to the hash declared by S3. These two hashes are not matching in your case, which means that the file stored in S3 is not the same as the local file.
My guess is that the log file is being appended to during the upload, and that this is causing the mismatch. Try first copying audit.log to another file, and upload the copy with s3cmd. Alternatively, only upload log files which have already been rotated.