I can only guess.
My first guess would be an aggressive (or buggy) firewall, anti-virus or security program. The Arduino Serial Monitor makes a localhost only network connection to the teensy_gateway program, which handles the USB stuff that can't be done from the Java-based Arduino IDE. Zone Alarm has often popped up warnings about network connections, even though it's localhost only networking. Maybe you have some other software like Zone Alarm that's silently interfering?
You could try downloading a fresh copy of arduino. Get the zip file, not the installer, and unzip it to a new location. Then install Teensyduino to that one. Perhaps reboot, then run the freshly installed copy. If it's a simple matter of the old one getting corrupted, that should do it.
If some sort of firewall or (lame) security product is interfering, well, you'll have to try turning that stuff off. Arduino and Teensyduino do not require any network connection to function, so you can unplug from the internet before temporarily shutting off security stuff to see if it makes a difference.
Of course, this was only a guess....