Or the usb-to-serial converter ? Which one do you use ?
You could re-install the Arduino IDE, or try the 1.5.8 BETA.
But I doubt if the Arduino IDE or the Pro Mini board causes this.
ADDED: After thinking about this.... Perhaps you are not uploading your sketch, or you have another Arduino connected to your computer. Can you try uploading a led blink sketch and check that it really does blink? Or you have a ATmega32u4 chip with some kind of funny auto baudrate.
Suppose the ATmega chip was damaged with a voltage spike, and the baud rate registers got damaged, while everything else is still working. I think that is not possible.
It is possible to blow the analog section on the chip and have the rest of the chip still working, but the analog section is a seperate section on the chip anyway.
Did something happen, or do you have something special ?
For example touching the Arduino with a loose wire with 9V, or do you have to much load connected to it, for example 10 or 20 leds, or a single led without resistor. Or do you have a weak usb power.
Did you try Arduino IDE 1.5.8 BETA ? Because it is more likely that something is going on on the computer than on the Arduino board.
Could you try another serial terminal program ? And another USB port and another USB cable. If possible, also another usb-serial adapter.
You could even try it on another computer.