If you suspect the PBX, confirm that by configuring an SPA112 to connect directly to a SIP trunk, bypassing the PBX. If you only need to test outgoing, the SPA can be set to not register, so it won’t interfere with production use of the trunk.
If it still fails without the PBX, you could test on a different internet connection, e.g. at home, or with a different trunking provider (many offer free trials).
However, given that Fax Pro is working reliably, now would be a good time to ditch the obsolete fax machine. See my post
Edit: Sorry, I missed your edit about bypassing the PBX. Paste a log of a failing call including a SIP trace, so we can check for transcoding or a similar issue. If that’s all clean we can capture traffic to see whether packet loss or excessive jitter is being introduced. If that also looks good we can capture traffic at the device or your router/firewall to see how the RTP is getting messed up.