We have a situation as follows:

1. We have a two different virtual machines (VMs) on some remote server farm. The machines are identical in terms of hardware/software(OS) configurations.
2. We have a J2EE application running on JBoss on each of those two machines.
3. These two applications are of different version sav V1 on VM1 and V2 on VM2.
4. We observed some degraded response time for application V2 when accessed via public URL.
5. When we accessed the application through a secured VPN, there is hardly any difference.
6. The bandwidth test (upload/download speed, ping etc) shows that VM1 is responding better when accessed via secured VPN.
7. We concluded that the application does not seem to have performance issue. Because, it that's the case the performance degradation should also be there when access via VPN. So we concluded its the network problem.
8. But since those two identical VMs are on same network we are looking for the reasons for different responses.

My question is, given the above situation, what could be reasons for such a behavior ?