I get two different outputs with "Digital 1D U8 1Chan NSamp"

I have two variations of a program that I am using to try and synchronize data collection at different rates.
Version A:
I have an anemometer attached to the DAQmx Create Channel (DI).vi
The Create Channel VI enters a while loop, and connects to DAQmx (Digital 1D U8 1Chan NSamp).vi, collecting 2000 samples
This create an output that feeds into a Build Waveform
The output of the waveform goes into NI_MAPro.lvlib:Extract Single Tone Information.vi to determine the dominant freqency of the pulses from the anemometer
The frequency gets multiplied through by a constant to determine the reading off the anemometer.
When I run this version of the program, I get that the windspeed is approximately 4-4.5 mph
However, I then needed to coordinate this 2-second collection rate with a photogate that is measuring rpm of a gear (60 teeth, approximately 20rpm, so pulses on about a 50ms cycle). I then created version B of my program
Version B:
Utilizes two While loops.
While loop #1: Just as in version A, but the reading off the anemometer at the end gets fed into a global variable (which is initialized to zero at the very start)
While loop #2: Uses a series of nested Case Structures to determine if the photogate has detected a new pulse, and if so, updates all outputs derived from the photogate data to determine what tooth we're on, the rpm, the time since the program started, and pulls the current value of the global variable.
Both While loops are slaved to a Wait Until Next ms Multiple delay of 1ms to try and synchronize the two loops.
Now, when I run this program, in the exact same conditions, I get a windspeed of about 8-9mph, and the values from the global variable update about every 4 seconds (which seems to imply that there's a related problem).
Can anyone help with this?
-G-

I'm sifting through the results for Time DIO (thanks for the quick suggestion). In the meantime, here are the two versions of the program. From what I've seen distant professional colleagues do, it should be fairly straightforward
Attachments:
Simple - Wind.vi ‏32 KB
RPM, Angle.vi ‏60 KB

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