When processing log files that end with a line feed/carriage return, the pipeline is unable to process the file. The work around is to open the file in some sort of text editor (Notepad++) and manually backspace the resulting blank line and saving the file. Then logstash immediately will process the log.
Is there a better way to process these files, the manual work around is tedious on large numbers of log files. "sed" also seemed ineffective, the notepad++ manual removal is the only way I've been able to figure out how to get these logs to process.