Impedance Analyzer Sweep Getting Interrupted

Hi Everyone,
I am working on a LabView program for an impedance analyzer which finds a peak and records data around the frequency the peak is located at. While collecting data about a certain peak it is also designed to continue tracking that peak because the peak is not constant. 
This program works in LabView Version 7, but this is not the case in Version 8.5. In 8.5, it looks like that the program begins sweeping (the little cursor on the display begins moving across the display) but gets interrupted and stops sweeping. This does not prevent the program from recording data - data is definitely being recorded. However, what this prevents us from doing is tracking the peak; eventually, the peak drifts off the span of the impedance analyzer and any data we collect is useless.Something I've noticed is that if I put LabView in "highlight execution" mode, the program works perfectly fine - no more interruptions! I'm not sure what is interrupting the sweep in normal mode - I'm relatively new to
LabView and attempted to use a WAITSRQ VI to remove any interruptions,
but this just ends up timing out.
While I have attempted tackling the problem from a programming point of view, the fact that this program works in version 7 but not 8.5 seems to indicate that it might not be a programming issue but rather something with the versions.
I have attached two files that may be helpful for anyone that looks at the problem. Mainly the problem is occuring when the control goes to the "Agilent4294APeakTracker_twochannel" file.The main file is the 4395A_no_curve_fit.vi file. If you have any questions about the program or anything I've been unclear about, please feel free to ask!
Thank you for your help!
Matt
Attachments:
4395A_no_curve_fit.vi ‏81 KB
Agilent4294APeakTracker_twochannel.vi ‏38 KB

Remember that this is all for your own good.  I am surprised this program ever worked correctly.  Dataflow, dataflow, dataflow.  The sequence structures you are using perform no function.  There is no coordination between your sub-vi and the main VI.  Your are sending commands from both VI's with no flow of the timing.  Review dataflow programming and clean up the VI, then you will be able to troubleshoot.

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