Sorry I missed your schematic in your 2nd post. But that diagram is pretty generic, and without actual component numbers it's anyone's guess if it is designed properly.
What voltage are you supplying Vcc from? What value does the voltage regulator regulate to (or at least it's P/N)?
Are the circuit's groundand the DAQ card digital ground tied together?
Have you tested this circuit by itself to make sure it works, at least statically. Use a DMM and make sure you get TTL compatible levels out when the photodiode is blocked and not blocked from the LED.
What wavelenght is the LED and photodiode sensitive to? If ambient (as opposed to IR) you could be picking up other light sources. If so, shield it from ambient light.
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"It’s the questions that drive us.”
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