Thanks gillham,
Looks good, I just did a quick sample with no inputs connected and channel 0 read High and the rest Low, I guess that pin has an internal pull-up assigned. Thanks for confirming the timing and increasing the sample size.
I found this and thought you my be interested:
http://www.easyvitools.com/rdesign/index.html
It is a bit too slow for our needs and looks old ( Help about says 2003 ) but is a great concept, if all you need is low speed switching and sampling. I am going to use it to do a Proof of Concept for the Bread-boarding tool interface. but I may have to write the target code myself to get the sort of performance I will need.
Is anyone out there aware of any other Control Panel / Virtual instrument tools that work with serial I/O ?
I have not managed to find anything customisable between this program on the low end and lab-view on the high end of the scale. They all seam to be designed to work with SPICE with no physical Real World interface or they are designed to work with dedicated hardware.
I did find a device that does provide all the functianality, but at a much higher speed and accuracy than I had in mind, with a corospondingly higher price tag too 
but I will include it here as It is a good target to aim for.
http://www.tina.com/English/tina/real_time_t_m
Cheers
Chris