At the school district where I work, we are trying to get rid of a T-1 line in between the two buildings, replacing it with a VPN over the faster internet connection. We set up two SonicWALL Pro 3060 firewalls (hooked directly into the modem), one in each school, and set up a VPN policy linking them. We then set up one computer on each firewall for testing the speed. With this direct connection, the transfer speed was about 2.5 Mbps, which is reasonable since the upload speed the ISP quoted to us was 5 Mbps overall.
However, when we set the firewalls up with IP addresses on our network's subnet (changing the VPN policy to allow for this) and set up the gateway to direct interschool traffic through the VPN, we were only able to achieve a transfer speed of less than 0.2 Mbps. What could be causing this bottleneck?

The hardware we are using is as follows:
2 Cisco 2651 routers, 1 in each school
2 SecureSchool appliances, 1 in each school

We are attempting to replace the Cisco routers with SonicWALL Pro 3060 firewalls, since all the routers are currently doing is file transfer over T-1.

I'd start with a traceroute from the PCs that you are moving the files between to ensure you are taking the path you expect.

Once you have verified that the path is going over the VPN the next question would be how are you testing the file transfer?

Are you useing windows via a drag and drop? or copy and paste?

For simplicity I'd try using FTP as a transfer, it will give you a better idea of the real transport capacity.

check the path and then use an FTP transfer and let us know if its any better.

File/folder sharing is too chatty; where you trying that?