If the RTP port ranges specified in the conf files are not respected (even after asterisk restart) that points to a possible asterisk issue. It's hard to imagine how the dahdi config module would have any influence over this, tho stranger things have happened.
The rtp ranges getting reset on upgrading the SIP Settings module sounds like a FreePBX bug, recommend filing a report at issues.FreePBX.org.
Difficult to say for sure, but the Firewall module sounds like it may be working properly, it should recognize the non default port range and allow the traffic. If Asterisk is not using these ports tho, it will be a problem.