Strange Linksys BEFVP41 Router Issue

Hello, We are running a VPN over 3 Linksys BEFVP41
VPN endpoints between 3 locations. We also use a Hand
Punch 3000 biometric time clock (
http://www.handpunch.com )

Everything except the Handpunch has no problem
traveling over the connection. We do FTPs, telnets, etc.
When we try to poll the time clocks however we get no
traffic at the server for the time clocks. any help would be
greatly appreciated.