Hi Paul,
I'd like to clarify a couple points in your post to make sure I understand your application correctly. It sounds like you want to generate a trigger pulse on the 6259 - is this using the counter or analog output? You also mentioned that you wanted your start trigger and reference trigger to be user-defined, but you are only getting 1000ms accuracy. This may be occuring because you may be using software timing.
It sounds to me like you'd like to use a digital trigger from your 6259 to start your acquisition, then specifying the number of samples to generate to control your Tx time. I may be missing something that you're trying to do in your application, so please reply with more details on your application if possible.
Thanks!
Daniel L.
Applications Engineer
National Instruments