I turned on debugging to see what is happening with the IKE negotations and saw this:
Seems as if there is a duplicate packet on the Azure side - is there a settting on the Juniper I can configure to change the timing on the packets that are sent?
## 2014-11-12 12:02:12 : IKESA LT timer armed, after <28740> seconds
## 2014-11-12 12:02:12 : install_ike_sa_key set ike sa crypto active.
## 2014-11-12 12:02:12 : cleanup seqno is 0
## 2014-11-12 12:02:12 : Delete IKEv2 conn entry...
## 2014-11-12 12:02:13 : IKE<104.45.x.x> ike packet, len 644, action 0
## 2014-11-12 12:02:13 : IKE<104.45.x.x> Catcher: received 616 bytes from socket.
## 2014-11-12 12:02:13 : IKE<104.45.x.x> ****** Recv packet if <ethernet0/6> of vsys <Root> ******
## 2014-11-12 12:02:13 : IKE<104.45.x.x> Catcher: get 616 bytes. src port 500
## 2014-11-12 12:02:13 : IKE<0.0.0.0 > found existing ike sa node 2abc050
## 2014-11-12 12:02:13 : IKE<104.45.x.x> Search IKE_SA table, found 2abc050.
## 2014-11-12 12:02:13 : Duplicated pkt checking ...
## 2014-11-12 12:02:13 : len in wind 616, hash in wind 2122461879, len 616, hash 2122461879
## 2014-11-12 12:02:13 : IKE<104.45.x.x> resend ikev2 packet
## 2014-11-12 12:02:13 : The sent ip is 104.45.x.x, port is 500
## 2014-11-12 12:02:13 : Can't send out pkt
## 2014-11-12 12:02:13 : Received duplicated pkt at Respnder
## 2014-11-12 12:02:14 : IKEv2: Aborted negotiations for IKE_SA(0x02a4b5a0/00010002) because the time limit has elapsed.
## 2014-11-12 12:02:14 : terminate sa v2
## 2014-11-12 12:02:14 : IKE<104.45.x.x> ike packet, len 644, action 0
## 2014-11-12 12:02:14 : IKE<104.45.x.x> Catcher: received 616 bytes from socket.
## 2014-11-12 12:02:14 : IKE<104.45.x.x> ****** Recv packet if <ethernet0/6> of vsys <Root> ******
## 2014-11-12 12:02:14 : IKE<104.45.x.x> Catcher: get 616 bytes. src port 500
## 2014-11-12 12:02:14 : IKE<0.0.0.0 > found existing ike sa node 2abc050
## 2014-11-12 12:02:14 : IKE<104.45.x.x> Search IKE_SA table, found 2abc050.
## 2014-11-12 12:02:14 : Duplicated pkt checking ...
## 2014-11-12 12:02:14 : len in wind 616, hash in wind 2122461879, len 616, hash 2122461879
## 2014-11-12 12:02:14 : IKE<104.45.x.x> resend ikev2 packet
## 2014-11-12 12:02:14 : The sent ip is 104.45.x.x, port is 500
## 2014-11-12 12:02:14 : Can't send out pkt
## 2014-11-12 12:02:14 : Received duplicated pkt at Respnder
## 2014-11-12 12:02:16 : IKEv2: 44c5130 azure-gateway reset DPD, no active p2 SA.