Cannot upload to Arduino Uno any more

Using Arduino IDE 1.x
5

Thanks for that huge hint. I had the same symptom, IDE would only download if user was root. If logged on as normal user I got:

Binary sketch size: 2,464 bytes (of a 30,720 byte maximum)
processing.app.SerialException: Error opening serial port '/dev/ttyUSB1'.
	at processing.app.Serial.<init>(Serial.java:178)
	at processing.app.Serial.<init>(Serial.java:77)
	at processing.app.debug.Uploader.flushSerialBuffer(Uploader.java:77)
	at processing.app.debug.AvrdudeUploader.uploadViaBootloader(AvrdudeUploader.java:172)
	at processing.app.debug.AvrdudeUploader.uploadUsingPreferences(AvrdudeUploader.java:67)
	at processing.app.Sketch.upload(Sketch.java:1706)
	at processing.app.Sketch.exportApplet(Sketch.java:1662)
	at processing.app.Sketch.exportApplet(Sketch.java:1634)
	at processing.app.Editor$DefaultExportHandler.run(Editor.java:2346)
	at java.lang.Thread.run(Thread.java:636)
Caused by: gnu.io.UnsupportedCommOperationException: Invalid Parameter
	at gnu.io.RXTXPort.setSerialPortParams(RXTXPort.java:171)
	at processing.app.Serial.<init>(Serial.java:163)
	... 9 more
processing.app.debug.RunnerException: Error opening serial port '/dev/ttyUSB1'.
	at processing.app.debug.Uploader.flushSerialBuffer(Uploader.java:101)
	at processing.app.debug.AvrdudeUploader.uploadViaBootloader(AvrdudeUploader.java:172)
	at processing.app.debug.AvrdudeUploader.uploadUsingPreferences(AvrdudeUploader.java:67)
	at processing.app.Sketch.upload(Sketch.java:1706)
	at processing.app.Sketch.exportApplet(Sketch.java:1662)
	at processing.app.Sketch.exportApplet(Sketch.java:1634)
	at processing.app.Editor$DefaultExportHandler.run(Editor.java:2346)
	at java.lang.Thread.run(Thread.java:636)

Deleting the user .arduino eliminated the Java exception but there was an avrdude problem. I solved the issue by copying .arduino/preferences.txt from root to the user .arduino directory.