Make sure you have installed the latest driver station and labview updates from
www.ni.com/first.
These updates have resolved some of the watchdog issues.
Here is my very broad understanding of watchdog issues at the moment. Each time the watchdog encounters an error it pauses your code running on the crio (watchdogs want to stop the machine from hurting itself if there is an error). If you call something in teleop.vi that is not opened in Begin.vi the whole control system will "pulse" in between pauses for example.
The update addressed this by making the watchdog ignore smaller errors. Ignore more small errors and you will have less watchdog errors. If you do something to cause a more "major" error you will still see watchdog timeouts.
Again, people who really know what the watchdog does are likely to wince at my explaination but it boils down to
-make sure the update is installed.
-make sure you have error free vis.
I think there was a "watchdog for beginners" explaination thread somewhere on the boards today ...