Ok, all the error messages have gone away after changing the A1 (flashed) card to the A2 (unflashed) in the machine on port 2. It was also able to pickup the SRP target straight away again.
The port 5 machine is not on so I am guessing that is why there are no errors from that A1 card. This is the machine with Windows 2012 Ess on it that will not work with SRP. I have now put Windows in a VM but the underlying ESXi also cannot see the SAN SRP target. The A1 card would not work at all with Windows unless it was flashed.
Hopefully there is a little tweeking that can be done with one of the firmware tools to correct this issue but I have no idea what that may be .