[astrodust]

Actually they can measure this with great precision. Consider how they were able to isolate the "Pioneer Anomaly" (http://en.wikipedia.org/wiki/Pioneer_anomaly), an extremely tiny amount of deceleration caused by radiation from the reactor.

If they can measure the drag caused by radiation, you can bet they can account for solar effects.

Also worth noting: The thrusters are fired very infrequently. According to that page, the Voyager missions required constant adjustments but the Pioneer system is spin stabilized.

[chton]

That's exactly the problem. Because Pioneer was spin-stabilized, it didn't need to fire thrusters, so the noise wasn't there and the anomaly could be measured. Voyagers aren't spin-stabilized, so they have to fire thrusters quite frequently. That makes it impossible to measure a small enough effect on them.