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The setup really is pretty simple.
There are two boxes. one at my home (two 35/35mb connections) and one in the DC which is on 1000/1000 (single NIC with multiple IPS).
I have two VPN connections setup on my home side each one going to a different IP address on the DC side. I then have a bond00 which the two VPN connections are apart of (on both sides).
BOND00 on home side is set to use IP 10.99.98.2
BOND00 on DC side is set to use IP 10.99.98.1
I then just have port forwarding for the local address 188.8.131.52 on the DC side (one of its multiple IPs) go to 10.99.98.2 (my home ZS box) which goes over the VPN.
It doesn’t surprise me that the second link will go slower for you. Like I mentioned one of my connections typically has a lot of upload activity going on it so the BOND is not very fast for uploading unless I shut down the activity using the bandwidth. This is due to the VPN bond being limited by the slowest connection in the MIX so if I am using 30 megabits out of 35 on one line then there is only 5 free and thus the bond will not go over 10 megabits.
Also the excessive PPS/ACKs also seems to cause high latency paths to be more effected compared to low latency paths.
This is why I suggested you limit the transfer to see what I am talking about and see how when going at the same speed one links will generate significantly more upload traffic (on your end, the downloader) than the other link. The only difference is that during the transfer it goes over the bonded VPN link (which of course you the downloaded has no way to know about).
I mainly use the bond connection for doing downloading and in that case the upload activity doesn’t effect it all that much.