Mach 3 ports and pins problems,

[JAZZCNC]

I don't know how the 2 channels are damaged have you any ideas what it takes to stop them working?

Well I pretty sure it won't be because of the ALM or ENA that's damaged the 5V Motor outputs because 24V General purpose Outputs are completely separate. And the ALM would be using Input's which are definately separate.
The Only thing I can think that would cause this is if you wired the Step & Dir wrong at drive and sent to ground. Because of the way the controller works using differential outputs then the Motor outputs are not isolated for performance gains. Unfortunatly this does come with some risk and is on the users head to make sure they wire correctly.

Read the Info about Differential signals either on Cslabs site, I think there is PDF manual installed when installing Plug-in etc check it out.

Personaly I would double check all connections and cables. Make sure you have channels set correctly and using correct pins for that channel. Then if sure they are blown send it back.
I've never known blown controller without it being caused by user error.! . . . But there's always a first time.!!!