These beeps you hear are when Windows starts and not during boot, correct?
The windows sounds are in the \Windows\Media folder. Changing those files is not easy to do. Are yours still there? Have you been running any other software that might have altered your normal setup?
Have you tried making any registry changes yourself that might have caused problems. I do not see registry entries for the sounds themselves, just file associations.
The Windows startup sound is in another file that has to be hacked to change. Were you attempting to do that?