If I have understood you correctly, you have SAP CI/PAS installed on node A and on node B you have DB installed. After the installation you did a failover of node A to node B and at this stage you get error related to message server. You did a failover of node B to node A and everything works fine.
Is ASCS part of the SAP cluster resources ?
Have you followed the installation guide recommendation for HA installation on Windows ?
Regards
RB