If you use vpn links standart netflow don't work with vpn links. You need use flexible netflow.
It works well with vpn links. Update your IOS if your router don't support it.
Example:
flow exporter NETFLOW1-EXPORTER
description NetFlow Analyzer
destination 172.16.0.1
source Loopback0
output-features
transport udp 9996
export-protocol netflow-v9
!
!
flow exporter NETFLOW2-EXPORTER
description Scrutinizer
destination 172.16.0.2
source Loopback0
output-features
transport udp 9996
export-protocol netflow-v9
!
!
flow monitor NETFLOW1
record netflow-original
exporter NETFLOW2-EXPORTER
exporter NETFLOW1-EXPORTER
cache timeout active 1
!
!
interface Tunnel12
ip flow monitor NETFLOW1 input
ip flow monitor NETFLOW1 output
!
!
interface FastEthernet1
ip flow monitor NETFLOW1 input
ip flow monitor NETFLOW1 output
link: http://www.cisco.com/en/US/prod/collateral/iosswrel/ps6537/ps6555/ps6601/ps6965/prod_white_paper0900aecd804be1cc.html