I don't know anything about your VPN service, whether it’s a MS VPN, who the provider is, etc., but some will relay ALL your local traffic over the VPN. That may have unintended consequences. For example, certain ports/services may be blocked by the VPN provider.
Unfortunately there’s usually no DIRECT way to control what does and doesn’t use the VPN. The only way I know to do this reliably is to keep your VOIP service on another machine (i.e., one not using the VPN). I know that may sound obvious, and perhaps not even practical. But you could achieve the same effect by using a VM (e.g., VirtualBox). You use the VPN in one OS (host or guest), and not the other. You then INDIRECTLY control which applications do and don’t use the VPN based the choice of OS.
Admittedly a bit of a hassle, but it would work. I just don’t know of any way of changing the VPN behavior other than w/ this type of workaround.