(1) If you installed Skype for Symbian client in your phone and use it to make VOIP calls, you can't record these calls. Boldbeast can't record VOIP calls, so it doesn't beep.
(2) If you didn't installed Skype for Symbian client in your phone and your friend call your phone number with Skype, the VOIP data will be routed to a local gateway, the local gateway will call your phone, indeed the call is just a normal phone call to you, Boldbeast will record it.
(3) If your E72 beeps during phone call recording, please set Beep Suppress to "Enabled", and do this:
(a) set One Side Beep Mode to "No", during call recording two sides will not hear beeps. or
(b) set One Side Beep Mode to "Yes" and use WAV format, during call recording you will hear beeps but the other side can't hear beeps.
Some E72/E52 works well in the case of (a), some other E72/E52 works well in the case of (b), please try it yourself.