Have you  tried to log the messages read from the pipe without the filter to a file and post an example of the log entries to this mailling list ?

I've a similar problem on AIX (5.3 ML3) where the system syslog daemon writes its messages to a named pipe
and syslog ng should read from it. But for some odd reason AIX syslog adds the FACILITY and LEVEL to the log message
which causes that the LEVEL field "shifts"  to the right.
Therefore Syslog-NG isn't able to parse this correctly, because it interpreted the FACILITY entry as program name ...