One thing you might want to do is use NI-SPY that ships with NI-VISA and see if you can figure out what may be going wrong. NI-SPY will show you a log of all of the VISA calls and the values that were returned from your application. This can help you evaluate if the correct data is being returned from each VI. One thing to look at is if you are using the bytes at serial port on a newer faster system it is possible that the bytes at port is returning before the instrument has had time to output any or all of the data. You might want to try inserting some delay before processing the bytes at port and possibly increase the timeout.
Another thing that was added in that time frame was synchronous and asynchronous reads. I would suggest using synchronous operations to more closely mimic old code.
KB 3D9B8E4B.
I hope this helps.
-Josh
