Absolutely, and the problem is in general getting worse as die sizes decrease. All but the very cheapest of satellites are now designed to have multiple avionics systems running in parallel. They vote on the incoming sensor data, vote on the outgoing commands, sometimes even on memory content. A computer that repeatedly steps out of line is voted off the island. This redundancy is danged expensive. It's there for a reason.
A somewhat recent example of an SEU causing a real problem: http://www.jpl.nasa.gov/news/news.cfm?release=2010-151. The Voyager spacecraft are particularly sensitive to SEUs because they are now running in single string mode (only one active set of avionics) to conserve power.