You may be experiencing the results of a programming error, or an old bug. Have you located the portion of code where the problem is occurring?
Also, did you upgrade to NI-DAQ 6.9.1? Have you tried the code in LabVIEW Real-Time 6i? Are you using SCXI? Which DAQ boards are you using?
Are you using serial, or GPIB? Are you doing File I/O? Which network communication methods are you using?
Does the controller hang, or reboot? Please describe the behavior in detail.