I guess the question is... does this not work when you are starting a fight against a new target and you are just experiencing lag from your main getting a new target and your alt knowing he has a new target
or is the problem exist when you main has had the target for several seconds and you alt still doesn't fire?

i personally would use something like this.
main
/castsequence [nochanneling] smite,mind flay,mind flay,...
alt
/castsequence [target=focus-target,exists,nochanneling] smite,mind flay,mind flay,....

then spam the heck out of the button.
if it's just a lag issue this spaming of the button will get you past the lag.