I am sorry i didn't check back with you noz LOL
I am not completely sure what it is, but eliminating the light (with new pots) will go a long way to stop it from spreading to your plants.
the green u seen is a type of root rot home slice its from ur clear cups, or white ones... just put em into a bigger pot that isnt see through and just get ur transplant over with as long as there big enough to handle it.