Do you using any special in the config? I using L2TP over native ethernet IF and Vlan IF also and I have stable L2TP connections on my RB4011 (ARM) and RB1100AHx2 (PPC) with 7.1RC4.
Here is my config about the L2TP client side:
ppp/profile/print where name="default-encryption"
Flags: * - default
2 * name="default-encryption" bridge-learning=default use-ipv6=yes use-mpls=yes use-compression=no use-encryption=required only-one=default
change-tcp-mss=no use-upnp=no address-list="" on-up="" on-down=""
interface/l2tp-client/print where name="L2TP"
Flags: X - disabled; R - running
0 R name="L2TP" max-mtu=1376 max-mru=1376 mrru=2564 connect-to=a.b.c.d user="pppuser" password="ppppass" profile=default-encryption
keepalive-timeout=10 use-peer-dns=no use-ipsec=no ipsec-secret="" allow-fast-path=yes add-default-route=no dial-on-demand=no allow=mschap2
l2tp-proto-version=l2tpv2 l2tpv3-digest-hash=md5
L2TP server side:
ppp/profile/print where name="default-encryption"
Flags: * - default
4 * name="default-encryption" local-address=10.1.1.1 bridge-learning=default use-ipv6=yes use-mpls=yes use-compression=no use-encryption=required
only-one=default change-tcp-mss=no use-upnp=no address-list="" on-up="" on-down=""
interface/l2tp-server/server/print
enabled: yes
max-mtu: 1384
max-mru: 1384
mrru: 2564
authentication: mschap2
keepalive-timeout: 10
max-sessions: 16
default-profile: default-encryption
use-ipsec: no
ipsec-secret:
caller-id-type: ip-address
one-session-per-host: yes
allow-fast-path: yes
l2tpv3-circuit-id:
l2tpv3-cookie-length: 0
l2tpv3-digest-hash: md5
accept-pseudowire-type: all
accept-proto-version: all
The 1376byte MTU is calculated to L2TP over IPSec tunnel on ISP's PPPoE.