Hi Jim,
The reinstall of 7.1 would not change the way the AI Read VI works. I assume this is the Traditional DAQ VI that you can select out of the function pallette and place down. The triggering characteristics of the data acquisition are determined by a different VI called AI Trigger Config.
I want to make sure we are clear on the terminology. When you say trigger, that would mean the initial acquisition would occur based on either the following or rising edge of the first square wave pulse. After that the internal clock just continues to acquire based on the setting you have input. The other option though is that you want to set which edge of the square wave every sample acquisition is done on and your clock for the acquisition is the external source. If that is the case, then I can see what you are reffering to in the AI Read.The conditional retrieval cluster, where the slope is located has a mode. Have you set that mode to on? That is something I could see affecting the behavior of your VI. Make sure when you save this VI, that you save it as another VI, and not actually save the VIlib file. Please let me know if there are further problems with this issue.
Have a great day,
Michael Denton
Applications Engineering
Nationa Instruments