Here are a few things to check:
1. On the host that you're only seeing 2 paths, have you verified that both of your vmnics are showing compliant and active on the VMkernel port bindings? I had an issue similar to this and found that one of the nics was showing non-compliant. It came down to the wrong vmnic was selected for the iSCSI vSwitch.
2.Double check to make sure that you have your physical link plugged into your iSCSI VLAN on your switches (if you have them split into their own VLAN)
3. If you're using jumbo frames, do you have the MTU set on the vSwitch and VM port group at 9000?
When you rescan for the additional paths, are you seeing any timeouts in the vmkernel logs? Or is it taking an extended period of time to scan from that host as if it's rescanning multiple times?