Hi Gordon,
Just checking my understanding of what you are trying to do.
You are generating an analog output waveform of constant period on your PXI 6466 which is outputted to a laser. You have 128 detectors and want to read 8 at a time using your multiplexer, switching at the start of each waveform period.
Would your multiplexer be a PXIe 2593 by any chance? What sort of waveform frequencies and input frequencies are you talking? A screenshot or upload of your code may be useful.
You're right, hardware timing may be of use in this case. If the generation and switching both run off the same internal sample clock, they will be synchronised.
http://www.ni.com/white-paper/11369/en/ You may find the 'Share Sample Clock Directly (Sample Clock Synchronization)' section in this whitepaper useful.
Are you using 'niSwitch Configure Scan Trigger VI'? One thing that might work would be to send a trigger each time a waveform starts. There is an example included in LabVIEW named 'Switch - Scanning with a DMM - Synchronous' that might be relevant .
Here is an example of reading multiple channels sequentially using DAQmx, which I see you already have managed to implement but it may be useful to compare to.
https://decibel.ni.com/content/docs/DOC-6901
Let me know if any of these are of use to you.
Thanks,
Leah