My furnace appears to go through it's sequence normally, but when the burners ignite they shudder and choke for 1 or 2 seconds and than everything appears to be okay after this. It almost seems like they are being choked out for a quick second and then brought back to life. Any idea what this could be? Dirty burners? I read something about these furnaces having problems with the control boards?

You need to clean it.