Same here, although the issue is slightly different.
Updated Mac Mini with server.app to 10.9.3, L2TP VPN still works my mac running 10.9.3, connects as normal.
However other clients (windows and android) would encounter error when trying to establish connection to server.
Windows client would fail wirh Error 789, previous to the update it was working.
May 18 18:58:13 mms.private racoon[413]: IPSec Phase 1 started (Initiated by peer).
May 18 18:58:13 mms.private racoon[413]: invalid DH group 20.
May 18 18:58:13 mms.private racoon[413]: invalid DH group 19.
May 18 18:58:13 mms.private racoon[413]: IKE Packet: receive success. (Responder, Main-Mode message 1).
May 18 18:58:13 mms.private racoon[413]: >>>>> phase change status = Phase 1 started by us
May 18 18:58:13 mms.private racoon[413]: IKE Packet: transmit success. (Responder, Main-Mode message 2).
May 18 18:58:13 mms.private racoon[413]: IKE Packet: receive success. (Responder, Main-Mode message 3).
May 18 18:58:13 mms.private racoon[413]: IKE Packet: transmit success. (Responder, Main-Mode message 4).
May 18 18:58:13 mms.private racoon[413]: IKEv1 Phase 1 AUTH: success. (Responder, Main-Mode Message 5).
May 18 18:58:13 mms.private racoon[413]: IKE Packet: receive success. (Responder, Main-Mode message 5).
May 18 18:58:13 mms.private racoon[413]: IKEv1 Phase 1 Responder: success. (Responder, Main-Mode).
May 18 18:58:13 mms.private racoon[413]: IKE Packet: transmit success. (Responder, Main-Mode message 6).
May 18 18:58:13 mms.private racoon[413]: IPSec Phase 1 established (Initiated by peer).
May 18 18:58:14 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:14 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:58:16 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:16 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:58:18 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:18 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:58:21 mms.private racoon[413]: IKE Packet: transmit success. (Information message).
May 18 18:58:21 mms.private racoon[413]: IKEv1 Information-Notice: transmit success. (Delete ISAKMP-SA).
May 18 18:58:23 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:23 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:58:31 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:31 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:58:47 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:58:47 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:59:04 mms.private racoon[413]: IKEv1 Phase 2 Initiator: dropped. (Can't continue Phase 2 without valid Phase 1).
May 18 18:59:04 mms.private racoon[413]: can't start the quick mode, invalid linked ISAKMP-SA
May 18 18:59:18 mms.private racoon[413]: IKE Packet: receive success. (Information message).