I have the same issue.
I have a Windows 2008R2 server set up to accept L2TP/IPSec VPN connections and a Synology NAS set up with both L2TP/IPSec and PPTP connections.
With versions prior to 9.3 PB1, all three connections worked. With 9.3 PB1, the Synology L2TP/IPSec connection fails, but bizarrely the L2TP/IPSec connection to the Windows server is still OK. I have borrowed a colleague's iPhone 5S with an older iOS version installed, and the Synology L2TP/IPSec connection works fine with that.
So... it's definitely an iOS 9.3 beta issue, but not as clear-cut as it might first seem.
Fingers crossed for a quick resolution.