OK, I tried to simplify things to determine where my problem is. As mentioned, stream MPX with flac should not be an issue, so I will leave that for now.
As command line stereo tool will not resample, I created a test file to test with using Audacity...
Input file: 192kHz, WAV/PCM (S16 LE), Stereo, 16-bits per sample.
I then ran the command './stereo_tool_cmd_64 input.wav output.wav -s fm.sts -V'
It runs and processes the file, I see the ascii VU meters moving about... Feeling good so far!
I then take the out.wav and load into MPXTool to analyze (It complains that it is a stereo file, so i load out.wav into Audacity, split to mono tracks, then remove one of them, and save it again...(Is this ok?) MPX tool will now look at my (hopefully MPX output file)...
Well, the output is not what I would expect!!! Pilot clearly missing
My sts file came from working DSP stereotool on windows... I guess/hope commandline ignores mentions of windows sound devices in there as I did just spot a mention!
@Edgar, My final aim here is to take a stream from our studio, do all stereotool processing and RDS/MPX, then have this available on myicecast server, so that my only actual audio output is a raspberry pi at my transmitter point! To create flac stream I plan to use liquidsoap with %ogg(%flac,...) etc. Once I get it working, I will make a clear guide on how to do it!! (I sent a pm to Radio700 to see if they will offer a little more assistance with how they are doing it!)