The only time I’ve seen something like this was during the 5.5 and beta 5.6 days. The problem that cropped up was that the installation of the yacscom.dll (ActiveX/COM) component was installed/configured by both Yahoo! Messenger and the web based client. With this particular problem if the web base client was run after Messenger was installed it had the potential to (re)install the yacscom.dll a second time and hose up the settings in the registry which caused Messenger to fail (often silently) when activating voice.
I know that some third party clients distribute older versions of the yacscom.dll. If you’re using Messenger AND using a third party client which erroneously installs and registers an older yacscom component you are quite likely to experience the trouble you’ve been seeing.