I have received the following error message as well running a Leonardo on Mac OS X 10.8.2 and Arduino version 1.03.
processing.app.SerialException: Serial port '/dev/tty.usbmodemfd141' already in use. Try quitting any programs that may be using it.
at processing.app.Serial.touchPort(Serial.java:119)
at processing.app.debug.AvrdudeUploader.uploadViaBootloader(AvrdudeUploader.java:201)
at processing.app.debug.AvrdudeUploader.uploadUsingPreferences(AvrdudeUploader.java:67)
at processing.app.Sketch.upload(Sketch.java:1671)
at processing.app.Sketch.exportApplet(Sketch.java:1627)
at processing.app.Sketch.exportApplet(Sketch.java:1599)
at processing.app.Editor$DefaultExportHandler.run(Editor.java:2380)
at java.lang.Thread.run(Thread.java:680)
What is interesting is the sketch will run. If I replace that sketch with a new one (using the OPEN command and a new sketch) I will sometimes get this error or not. In any event the new sketch will run. That is sometimes the IDE will state Upload complete and other times the IDE will state the above error message. I have rebooted the computer to ensure that the port is identified. I have tried all the .tty ports with the same result.