First I would suggest upgrading to version 2.6.2 on both the controller and the APs. We have made some changes around these functions that should help quite a bit. You can reference the Upgrading BlueSocket vWLAN Controllers and Access Points for information on how to do this.
In general, switching SSIDs (or L3 networks) may not be extremely seamless because of the IP change. Many mobile units may not properly release their IP address. We have made some adjustments to try to "encourage" the clients to properly do this with de-authentications, etc. However, there are still some clients that have trouble with the change. I would suggest providing your use-case as well so we can better understand if there might be a better configuration option for these networks that may be smoother for your users.