I am unable to compile sketch on Arduino IDE 1.5.5-r2 for the COM3 and COM4 exposed aren't free.
Starting whith IDE 1.0.5 with Arduino Uno the 18 COM port is accessible also to IDE 1.5.5-r2 but at the end of compilation Java crash.
YOu probably have to provide way more information about your overall setup in order for anyone getting a faint idea of why this might happen. I am using 1.5.5r2 on Windows 7 Ultimate 64bit for weeks now and it just works fine, for all the Arduinos I am currently playing with (Uno, Mega2560, Leonardo, Yun), regardless of which port they are connected.
Just as a shot in the dark, are you certain to run the latest Java version (on whatever OS you are running)?