If it happens only within Money, check the sound configuration for events within that program and make sure that the sound files used for each sound that is enabled are indeed on the system in the place where Money is looking for them.
Likewise, when beeps occur outside Money in a running system, it may be that some program running in the system is trying to play a sound but cannot find the required WAV file. As a last resort, it may play the PC speaker instead. Any application can beep the speaker, even though that is very rare these days.
Beeps indicating motherboard problems only occur in POST (power-on self-test), not on a running system. If the system beeps before you even see a Windows logo, something is wrong, e.g., no keyboard or monitor has been detected, etc.