The problem is with your code, which you have failed to post (use the code tag # in the tool bar when posting). Perhaps you are using Serial.write instead of Serial.print. Below is some simple serial test code.
// zoomkat 7-30-11 serial I/O string test
// type a string in serial monitor. then send or enter
// for IDE 0019 and later
String readString;
void setup() {
Serial.begin(9600);
Serial.println("serial test 0021"); // so I can keep track of what is loaded
}
void loop() {
while (Serial.available()) {
delay(2); //delay to allow byte to arrive in input buffer
char c = Serial.read();
readString += c;
}
if (readString.length() >0) {
Serial.println(readString);
readString="";
}
}