Hint: Serial.read() will return a value whether there is something to be read or not. RTFM: Serial - Arduino Reference XD
So I'm still not following, the XBees aren't in the picture at this point?
This is another reason I prefer API mode to AT mode. Debug messages can be intermixed with the XBee frames, and because they don't contain the start delimiter, the XBee ignores them. But you could use Software Serial to write debug messages to I suppose.