I had the same problem when bonding 2 NICs from our 4 port 3com. Our onboard NICs would bond and achieve full bandwidth (or 40MB/s as the upper limit in the settings). Any of those ports on that 3com card would not go over 100Mbit (bonded or not).
I suspect it was a driver issue. We have replaced those cards with others and solved the problem. Those same cards work at 1Gbit in Windows boxes.
Since the recommended limit is 40MB/sec for replication, bonding won't give you more speed, just redundancy. Because of that we opted to have a single NIC dedicated to replication traffic and it easily hits the 40MB/sec limit.
I should also add that I was specifically told by Open-E support to not increase the 40MB/sec limit, unless using 10Gbit cards. Some sort of limitation of the underlying sync protocol (can't remember the exact explanation)