At one of my sites where Lync has been deployed as a replacement for a PBX I ran into an issue with the receptionist being able to answer and or transfer calls from the PSTN. Calls would come in, and about 30% would be problematic. Some, she couldn't answer at all, others, would either drop when she tried to transfer them, or would connect only after 45-60 seconds of silence, by which time, the caller would assume the call had been dropped and hang up. As you can imagine, this was having a significant impact on our ability to do business.
I researched online, and didn't really find any reasonable explanations or solutions. So, I opened as case with Microsoft Premier Support, and as we were working through testing, pulling logs from the SBA, Front End Servers and the receptionist's Attendant Console, we determined that what was happening was that the SIP REFER method was failing. Information on what the SIP REFER method does can be found at: RFC 3515 - SIP Refer Method..
After some more research, I discovered that SIP REFER is enabled by default in Lync, and the Gateway we have deployed, the NET UX 2000, does not support SIP Refer. I found this article on NET's website that explains how to disable SIP REFER, and as a result, Media Bypass: Disable Refer Support (required for Transfer).
The Microsoft article on this is found here: Configure a Trunk Without Media Bypass. The MS article lacks a great deal of information, and barely mentions the SIP REFER option.