Fibre connection problem

I wonder if anyone out there can help shed some light on a major problem we are experiencing?? I am a server person but our network guys don¿t know how to fix it and we need help.

We have 2 sites, about 2 kilometres apart, and we connect through a 1Gb fibre. We have 2 fabrics using Brocade 5000 switches and the long wave ISLs are connected into a Smartoptics box at each site.
About three weeks ago, for reasons unknown, we lost the link to our remote site and when it came back only half the ISLs were working:

At each site we have:

1 Smartoptics for the Brocade switches/Clariions
2 x CWDMs for Cisco network

The SAN connections were through the Smartoptics, but now none of the ISLs work. If we put the 4 x ISLs into the first CWDM only the ¿blue¿ works. If we put the ISLs into the second CWDM only the blue and grey work.

The violet and green don¿t work at all, but all colours from the Cisco switches work in all three. We bought more coloured GBICs and tried adding extra ISLs to the Brocade switches, but none of them work through the Smartoptics or CWDMs.

We have replaced cables, reboot the Brocade fabrics, changed the speed of the ports and prayed, but still only the grey and blue GBICs are working. This means we have one link through each fabric. The fibre cables have been tested by our supplier and passed OK.

Any suggestion greatly received.