What you are talking about is pure transmitter problem. You just need clean MPX input. That transmitter probably does not have it and you just need to make one.
Even if you think you can fix problem it that way whole point of clipping/composite clipping is lost.
The transmitter uses a BNC port for the MPX input
It seems that the port is made for RDS, SCA and other higher frequency signals, not necessarily for the mono audio signals.
The MPX signal is shown here, you can see that from 0-~1000Hz, the signal is severely attenuated.
Compared to other stations, these frequencies are much higher:
Here is the circuit, and it would seem this is all done by design:
The capacitors there would seem to be the cause of the low frequency attenuation as they are not present on the line in path. Now I have no issue desoldering these capacitors and running a jumper there, but seeing as how this is the way the transmitter was designed (and not knowing if this would cause RFI to be allowed in), and seeing as how this is a piece of software designed to modulate transmitters, I would venture to guess it would be more proper to allow the software to run different configurations. Ultimately I can understand how most people would not use a feature like this, but I could still see it coming in handy if someone wanted to use the same soundcard to modulate the same station, both AM and FM for example.