I'm glad to hear that you were able to use that work around for the time being. I will make sure that R&D is made aware of this issue. Hopefully it will be fixed in a future release of DAQmx/LabVIEW.
It looks like you are not able to use the built in timing source. One possible workaround is to call an exe (with System Exec.vi and "Wait until completion" set to False) in the main application TimingSource-DAQ.exe before exiting it with the Quit LabVIEW function, and this called exe will kill the process of the main application by using System Exec.vi too with the "taskkill /f /im TimingSource-DAQ.exe" command line.
Brian, if you need synchronization in a future application you could use this method as well. Its not the best solution but hopefully it will work until it is fixed.
Justin Parker National Instruments Product Support Engineer