At our office, we've been having this problem for some time, and I haven't found a solution for it. Some of our employees have a work phone at home, that is a Samsung IP telephone (SMT-i3105), that establishes a VoIP connection to our Samsung OfficeServ 7200 at our office, and the connection has to go through our MikroTik router.
Then we also use VPN connections (L2TP/IPsec) to access our NAS remotely and for Remote Desktop.
The problem occurs, whenever someone connects through the VPN connection, their VoIP connection will be lost, and the phone will disconnect, and when you disconnect from the VPN, the phone will work normally again.

The following ports and NAT rules are opened and set:
6000 UDP = IP data SIP connection
9000 UDP = IP connection setup
30000-30030 = IP MGI channels

Does anyone have any ideas, as to how to configure the router, for it to distinguish the 2 different connections, the VPN one, and the VoIP one, and so that both can work at the same time and has anyone had similar issues?