We have a similar issue at our end too with PPPOE WAN and L2TP/IPSEC VPN.
We basically have a RB951G-2HnD with LT2P/IPSEC configured, that is connected to the internet via a PPPOE connection to a bridged modem
Following a reboot of either the modem or the mikrotik router the PPPOE connection would not be able to connect again.
The only way we found to revive the PPPOE connection is to disable the L2TP server from the PPP section on the mikrotik (disabling the VPN).
Any help on this matter would be greatly appreciated.