I have the following configuration:

define DEFAULT_OUTPUTS null_output

include c:/Program Files (x86)/nxlog/conf/nxlog.conf.d/\\*.default

<Extension app_log_multiline>
  Module xm_multiline
  HeaderLine /^[0-9]{4}-[0-9]{2}-[0-9]{2} [0-9]{2}:[0-9]{2}:[0-9]{2}\.[0-9]{3}/
</Extension>

<Input app_logs>
  Module im_file
  InputType app_log_multiline
  RenameCheck true
  File "C:\\ProgramData\\App\\EventLog\\TestFile.log"
  Exec $type = 'windows_log_files';
  Exec $Message = $raw_event;
  Exec $file_path = file_name();
</Input>

<Route r_app_logs>
  Path app_logs => testfile
</Route>

and

<Output testfile>
  Module om_file
  Exec to_json();
  File "C:\\testlogoutput.txt"
</Output>

If the log file contains the following lines:

2016-09-15 02:00:37.906 TestEvent
2016-09-15 02:00:42.251 TestEvent2

with an empty line after the second log line, the output is correct:

{
    "EventReceivedTime":"2016-09-19 22:35:32",
    "SourceModuleName":"app_logs",
    "SourceModuleType":"im_file",
    "type":"windows_log_files",
    "Message":"2016-09-15 02:00:37.906 TestEvent",
    "file_path":"C:\\ProgramData\\App\\EventLog\\TestFile.log"
}
{
    "EventReceivedTime":"2016-09-19 22:35:32",
    "SourceModuleName":"app_logs",
    "SourceModuleType":"im_file",
    "type":"windows_log_files",
    "Message":"2016-09-15 02:00:42.251 TestEvent2",
    "file_path":"C:\\ProgramData\\App\\EventLog\\TestFile.log"
}

However, if the log file contains the same two lines as above, without an empty line after the second log line, the output becomes:

{
    "EventReceivedTime":"2016-09-19 22:40:59",
    "SourceModuleName":"app_logs",
    "SourceModuleType":"im_file",
    "type":"windows_log_files",
    "Message":"2016-09-15 02:00:37.906 TestEvent\r\n2016-09-15 02:00:42.251 TestEvent2",
    "file_path":"C:\\ProgramData\\App\\EventLog\\TestFile.log"
}

Basically, unless there is an empty line after the final log event, it seems that multiline is combining the last two lines into one, even though the HeaderLine is matched correctly.
Did I configure something wrong?