What does that reset do? The reason I ask is a ran across a similar issue.
I programmed a little test program to test an odd baud rate output from the UNO and loaded it. Everything went fine and the serial program worked, and I finished my test. My goal was just to see if I could program non-standard baud rates and get the proper output, turns out I can.
The problem comes when I try to load anything else onto the board, the serial port in the Tools menu is grayed out and serial commands fail to the USB interface.
I did a search on the problem and tried a number of solutions, nothing seemed to work.
I finally took a virgin Atmel chip with the Arduino bootloader and replaced the chip on the UNO, then I got the serial port set and the menu working. I was then able to return the "failed" chip and get a non-serial data program loaded.
How do I program a serial application using the serial port and not risk locking up the board? I really don't want to run through this rain-dance every time I want to use the serial port!