The thing is, if you disable the system speaker in windows, it disables Windows ability to use the speaker. Windows does not have specific beep codes. The BIOS has specific beep codes and regardless if you disable it in windows, the BIOS still has access to it and will continue to create beeps, if it is in fact a BIOS/Hardware issue.
In any case, review your event logs.
Also, if this is a Dell, see if it is OMCI compatable install the driver for it, this allows the BIOS to relay events to windows to report visually what the error may be (I.e.. Chassis intrusion, thermal event, etc..)