First thing.
Get rid of the shift registers on the error wire. I find they are a bad idea. (Others might disagree.) Yours is a perfect example why those shift registers are bad.
Right now you have no idea if that timeout error is some random, odd occurrence, or something that will persist. Maybe it just happens rarely, but the next VISA read will work fine. With the shift register, once you have an error, it will persist forever without any special code to do something else or clear the error. That error goes to the beginning of the next loop iteration. All the VISA commands have standard error input functionality which means they won't execute if there is an incoming error. They all do nothing and just pass the error message on. And the next loop iteration gets it, and it goes on forever until you stop your VI and restart.
Make those error wires normal tunnels. Put an indicator on the wire so if something does happen, you can see it on the front panel. Perhaps create a logging function that if there is an error, it rights the date, time, error message to a file that you can review later to see how frequently the errors occur.
