How do I set up my timer/clock for a 17 bit synchronous encoder?

I am trying to get an output from a 17 bit Gray Code encoder. I need the position output for other projects.
Here is a list of equipment being used:
PCIe 6361
CP-850-17S-GC-CW encoder from Allied Motion
SCB-68
I am trying a 3 wire connection.
Clock + to PFI 12
Data + to AI 0
NSL - to +5 V
NSL+ to AI Gnd
Data - to AI Gnd
Clock - to D Gnd
I have used MAX to build clocking to the PFI 12 and can see the clocking. This is also what is coming out of my encoder. It does not apperar to synch up using continuos clocking.
I have tried to build a VI and use DAQmx with the same results.
When I tried to run N samples using 17 bits with a clock at 100KHz and an initial delay the signals, using an osciliscope, appear to be correct except that it does not change with the rotation of the encoder. The output of the encoder still appears to be the clock signal.
I have used other programs and they give the angle fine.
It may be I need to add something else and or set this up in sequence. If anyone can direct me to documentation I would greatly appreciate it.
I have added the documentation, from the website, for the CP850 17S GC encoder. This has the timing information. 
Attachments:
CP-800-900_Specifications_R1a(scrn).pdf ‏216 KB

Hi msmith
You are using a PCIe-6361, you could use that card also to acquire the same signals that you are generating. First you need to check that you are generating the signals as that encoder require, with the same PCI you can verify that. Then if you are generating the signals correctly, the enconder should has an output as shown in the graph in the datasheet, if not there is a problem in that enconder. 
*Other detail, I am not sure in this case but in other cases that I remember with other encoders, there is necesary to change the NSL from 1 to 0 for each value. You can try also to manipulate that input from the PCI-card.
Regards

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