What you are asking, I think, is can you control the A/D process within the serial port? You want to be able to more or less sample the analog waveform suitably fast and then determine the data and timing yourself.
I'm not sure how the other software you mention works, but given Labview's I/O abstraction layer, you are a bit removed from the serial port and it's hardware specific quirks. However there are additional serial port functionality hidden in the property node items. For example if you go to the serial communication palette and drop "bytes at serial port" on a diagram and then right click on the header, there is a bunch of more advanced features available there. This is how to gain access to things like DTR lines etc.
I'm wondering if you could do a bit banging sort of kludge where your input would actually come in on say DTR and you query that very fast in software. It would be like a 1 bit a/d which you are sampling in software. This sounds really nasty now that I've typed it out, but may do the job.
Also, don't forget your soundcard, it's a great high speed two channel AC coupled ADC.
Sheldon
Technical geek, engineer, research scientist, biodegradable...