I recommend you drop the "nomod" from your macro. It isn't needed and maybe causing the problem. New macro:

#showtooltip
/cast [mod:ctrl,target=focustarget,exists] Chain Lightning; [mod:ctrl] Chain Lightning; [target=focustarget,exists]Lightning Bolt; Lightning Bolt

The extra CL and LB I added are redundant but shouldn't hurt. In your setup, does even the main have a focus target? I use a focusless setup so I don't remember how it works when you use a focus system.