The spec says that BufferedReader.readLine() considers only "\r", "\n" and "\r\n" to be line separators. We must not permit additional separator characters. I admit that the RI's behaviour is surprising, and incompatible with it's own Pattern and Scanner classes. But this is the specified behaviour; the doc explicitly calls out which character sequences are used as newlines. It does not permit additional characters to break lines.
For users reading EBCDIC-encoded files, a better practice is to read through the files using a Scanner. That way, the application will behave the same when executed on either Harmony or on the RI.