at each site we are using satellite connection
tunnel for VPN
This is your problem. Satellite has terrible latency (it takes a while for the data to go all the way up to the satellite and back down again). This means that things like TCP never open the window and remain in slow start at horrible throughput rates and would never get to use the full bandwidth. To help fix this, the satellite internet providers use various hacks on the protocols (like intercepting the TCP streams and sending Acks from the modems). This usually works well but it requires the intercepting device to be able to see and understand the packets. IPSec VPN traffic encrypts the packets so that the intercept devices cannot see what is going on and "accelerate" the connection.
The only way out of this is going to be either to drop satellite and move to something else or drop IPSec VPNs and move to a tunnelling technology that the accelerator boxes can understand (you'l have to talk to the satellite provider on if they support any tunnelling protocols).