It sounds like you are using Serial.write() which will only send 8-bit values. Perhaps you want to use Serial.print(). That will send a series of ascii digits which can be converted back into an integer value at the PC end.
Oh, no. I want to send 1000 bit values TO the arduino. I have no problems having the arduino send large values to java. I just send them as strings and convert.
It's an issue because I want to send degree values to servos, so if I want to say, send 179 to a servo, I have problems.