I have seen this on a couple small clusters we have upgraded to 5.0... Faxes/modems worked before, without T.38, and not they don't, but not at every site. Two sites are networked over a hardware VPN over the public Internet (20-25ms ping times between controllers), both of those fail now where they worked before, and one site has direct fiber connection about 30 miles at 1GB (2-4ms ping times between controllers) and that works just fine. Tech support essentially gave me the same run around, "analog dial-up data services are not supported over IP trunks... <click>".
Guess I just chocked it up to the newer software has some different timings or uses to many system resources and causes these very time dependent connections to fail. Newer isn't always better I guess, but if you find a solution let me know. For these customers we essentially just made them use the PSTN trunks they have for those services, and it worked OK since they were very limited use devices.