louhaven
1) Please describe completely the network arrangement of your SME server, the managed switch, any firewall & where devices are located in the data flow.
2) What mode is your SME configured for ie, private server, server only, server & gateway, (in server & gateway mode is it in Static IP configuration or not) ?
3) What type of modem & configuration is between SME server & Internet ie bridged modem ?
4) You mention the ata, I assume you mean an Analogue Telephone Adapter (ATA), correct ? .... and to that you attach an old style PSTN (analogue) phone rather than an IP style phone ?
5) You mention the managed switch & that it prioritizes VOIP traffic. That may all be very well, but if that switch is connected to the LAN side of SME server then you also need QoS (traffic shaping & priority for VOIP) on SME server.
6) As requested can you paste your iptables &/or template contents to a image site etc & post a link here.
7) For some years I have used an ATA on the LAN side of an SME server (connected via the local network hub), with SME in server & gateway mode (with Wondershaper) & it worked fine. From memory I did not need to make additional changes to the SME server firewall settings, or open ports.