Did the VoIP phones even work with this software revision? Here's what my 4.1 manual says about IP phones:

IP phones using the H.323 Revision 2 protocol will work with the Discovery VoIP card. The IP phone, however, will not be integrated into the system. Instead, the IP phone resembles a single-line telephone that uses the Internet or other IP network instead of the PSTN. IP phones allow dialing using the IP address of the destination system...

I don't know, I've worked on very few Triad systems.

Having said that, have you tried making things work on site? Whenever I have trouble with ANYTHING IP, I start working with it on the local area network. That way you can rule out any issues with firewall, router, etc...