How to get EXTMUX to pulse only when taking samples, and not on LocalMUX Change? (E Series Board)

I am using the 6031E series board. The EXTMUX is setup to pulse on each convert pulse. While taking data, I am getting a pulse on the EXTMUX for each sample taken, and a pulse for each time the 6031E switches its own internal mux. Is there anyway to only have the EXTMUX line pulse ONLY when a sample is taken, and not when the internal mux switches?

If you are reading the DAQ-STC manual, the signal I am talking about is the EXTMUX. If you are reading the PCI E Series manuals, the signal I am talking about is called SCANCLK (just to make things easier to understand, I guess??). The EXTMUX is setup through the MITE, and will pulse after every convert signal. My problem is that it also pulses when the internal mux changes as well.
So (for simplicity), if I wanted 2 channels, with 5 samples on each channel, and a mux outside the card on each line, the EXTMUX signal would sync the external hardware with the card/software.
In theory I would expect 10 pulses on the EXTMUX/SCANCLK pin, but in reality I get 12 pulses. If I had 3 channels, 5 samples per channel, (Expected 15 pulses) I end up getting 18 pu
lses in reality. This throws off any kind of sync to the outside world.

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