L2TP over IPSec looks exactly the same as IPSec to a provider. It is all encrypted.
I'm going to guess an MTU squeeze. Try this experiment; use this command on one machine at one of the sites to display all your interfaces:
netsh interface ipv4 show interfaces
Note the interface number that is configured with the IP address used for communication. Lets pretend it is interface 10.
Then issue this command (change 10 to your interface number):
netsh interface ipv4 set subinterface "10" mtu=1400 store=persistent
To undo this repeat the command with an MTU of 1500
If this solves it, then do this command on the servers that everyone connects to (rather than having to do it on all the workstations).