l2tp vpn issue

Have you tried setting a route, manually, on Windows on how to get to the other network?
May help

windows ip 192.168.12.2 gw 192.168.12.1

from windows i can reach all linux interfaces

Is routing activated?
What is the content of your routing table? (command: ip r)

root@vpnserver-Name:~# route
Kernel IP routing table
Destination Gateway Genmask Flags Metric Ref Use Iface
default 192.168.1.1 0.0.0.0 UG 0 0 0 eth0
R3000-2G * 255.255.255.255 UH 0 0 0 ppp0
192.168.1.0 * 255.255.255.0 U 1 0 0 eth0
192.168.12.0 * 255.255.255.0 U 1 0 0 eth1
root@sreejith-System-Product-Name:~# ifconfig
eth0 Link encap:Ethernet HWaddr 00:00:00:00:01:f8
          inet addr:192.168.1.100 Bcast:192.168.1.255 Mask:255.255.255.0
          UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
          RX packets:3699 errors:0 dropped:0 overruns:0 frame:0
          TX packets:3015 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:3467288 (3.4 MB) TX bytes:486151 (486.1 KB)

eth1 Link encap:Ethernet HWaddr 00:50:ba:cd:4d:b7
          inet addr:192.168.12.1 Bcast:192.168.12.255 Mask:255.255.255.0
          UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
          RX packets:0 errors:0 dropped:0 overruns:0 frame:0
          TX packets:47 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:1000
          RX bytes:0 (0.0 B) TX bytes:8420 (8.4 KB)

lo Link encap:Local Loopback
          inet addr:127.0.0.1 Mask:255.0.0.0
          UP LOOPBACK RUNNING MTU:65536 Metric:1
          RX packets:273 errors:0 dropped:0 overruns:0 frame:0
          TX packets:273 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:0
          RX bytes:35912 (35.9 KB) TX bytes:35912 (35.9 KB)

ppp0 Link encap:Point-to-Point Protocol
          inet addr:172.16.1.1 P-t-P:172.16.1.30 Mask:255.255.255.255
          UP POINTOPOINT RUNNING NOARP MULTICAST MTU:1280 Metric:1
          RX packets:4 errors:0 dropped:0 overruns:0 frame:0
          TX packets:3 errors:0 dropped:0 overruns:0 carrier:0
          collisions:0 txqueuelen:3
          RX bytes:87 (87.0 B) TX bytes:60 (60.0 B)

rroot@vpnserver-Name:~:~# ping 172.16.1.1
PING 172.16.1.1 (172.16.1.1) 56(84) bytes of data.
64 bytes from 172.16.1.1: icmp_seq=1 ttl=64 time=0.047 ms
64 bytes from 172.16.1.1: icmp_seq=2 ttl=64 time=0.043 ms
^C
--- 172.16.1.1 ping statistics ---
2 packets transmitted, 2 received, 0% packet loss, time 999ms
rtt min/avg/max/mdev = 0.043/0.045/0.047/0.002 ms
root@sreejith-System-Product-Name:~# ping 172.16.1.30
PING 172.16.1.30 (172.16.1.30) 56(84) bytes of data.
64 bytes from 172.16.1.30: icmp_seq=1 ttl=64 time=979 ms
64 bytes from 172.16.1.30: icmp_seq=2 ttl=64 time=380 ms
^C
--- 172.16.1.30 ping statistics ---
3 packets transmitted, 2 received, 33% packet loss, time 2000ms
rtt min/avg/max/mdev = 380.295/679.981/979.668/299.687 ms

=================================================
windows route
----------
Active Routes:
Network Destination Netmask Gateway Interface Metric
          0.0.0.0 0.0.0.0 192.168.12.1 192.168.12.2 20
        127.0.0.0 255.0.0.0 127.0.0.1 127.0.0.1 1
       172.16.1.0 255.255.255.255 192.168.12.1 192.168.12.2 1
      192.168.1.1 255.255.255.255 192.168.12.1 192.168.12.2 1
     192.168.12.0 255.255.255.0 192.168.12.2 192.168.12.2 20
     192.168.12.2 255.255.255.255 127.0.0.1 127.0.0.1 20
   192.168.12.255 255.255.255.255 192.168.12.2 192.168.12.2 20
        224.0.0.0 240.0.0.0 192.168.12.2 192.168.12.2 20
  255.255.255.255 255.255.255.255 192.168.12.2 192.168.12.2 1
  255.255.255.255 255.255.255.255 192.168.12.2 3 1
Default Gateway: 192.168.12.1
===========================================================================

ping reply frm windows

C:\Documents and Settings\SreejithLohithakshan>ping 192.168.1.100

Pinging 192.168.1.100 with 32 bytes of data:

Reply from 192.168.1.100: bytes=32 time<1ms TTL=64

Ping statistics for 192.168.1.100:
    Packets: Sent = 1, Received = 1, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 0ms, Maximum = 0ms, Average = 0ms
Control-C
^C
C:\Documents and Settings\SreejithLohithakshan>ping 192.168.12.1

Pinging 192.168.12.1 with 32 bytes of data:

Reply from 192.168.12.1: bytes=32 time<1ms TTL=64

Ping statistics for 192.168.12.1:
    Packets: Sent = 1, Received = 1, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 0ms, Maximum = 0ms, Average = 0ms
Control-C

C:\Documents and Settings\SreejithLohithakshan>
C:\Documents and Settings\SreejithLohithakshan>ping 172.16.1.1

Pinging 172.16.1.1 with 32 bytes of data:

Reply from 172.16.1.1: bytes=32 time<1ms TTL=64
Reply from 172.16.1.1: bytes=32 time<1ms TTL=64

Ping statistics for 172.16.1.1:
    Packets: Sent = 2, Received = 2, Lost = 0 (0% loss),
Approximate round trip times in milli-seconds:
    Minimum = 0ms, Maximum = 0ms, Average = 0ms
Control-C
^C
C:\Documents and Settings\SreejithLohithakshan>ping 172.16.1.30

Pinging 172.16.1.30 with 32 bytes of data:

Request timed out.

Ping statistics for 172.16.1.30:
    Packets: Sent = 1, Received = 0, Lost = 1 (100% loss),
Control-C
^C
C:\Documents and Settings\SreejithLohithakshan>