Two problems related to noises during shifting have been reported for the 2004 Toyota Matrix. The most recently reported issues are listed below.
Started making loud noise, then locking up. Could not shift or get into gear.
2004 Matrix transmission failed while wife was driving on highway on a rainy night. Prior to this the transmission began to have noises which one might attribute to an auto at 110,000 miles. After this failure transmission would not shift except with great difficulty. I had the Matrix towed home and am in the process of determining solution. The rest of the car is flawless but this early failure of a manual transmission in a Toyota is discouraging. The situation was a dangerous one as failure of the transmission caused those vehicles around her to become aggressive towards the slowly moving Matrix. My wife was extremely fortunate to coax the car to safety. These unexpected repairs will cost me around $2500 to $3000 to resolve. The auto is of no value without the repair, and with the repair resale not much greater.