occasional repetative beeps on boot

Hi, the issue that I am having is with a supermicro superserver, it is running Ubuntu 9.04 64 bit, when it is booting up just before the login screen I get a very fast repetative beep coming from the machine( not every time only approx 50% of the time), it doesn't change in anyway . The machine doesn't crash at all I am still able to log in and use the machine but the beeping doesn't go away. I have checked all aspects of the build of the machine i/e the seating of memory and cards and the bios revisions. I also swapped the drive and ran it with windows xp and there was no beeping and no issues at all which is suggesting a Ubuntu issue. I am pretty new to using this so would appreciate as much support as possible.

Thanks