The idea is to figure out what is happening. The macro is correct as you have already seen, so you have to do some snooping.
When you push the macro, does the pally get the mob soon enough to make sure the judgement isn't failing? You say he is auto-attacking. What happens if you push the macro 2 secs after you get a mob? Pick a mob that won't hurt you for 30 secs but still has some hitpoints. Pick the mob on your main. Push the macro when you are 40 yards from the mob. Does the pally always target the mob? You should hear, not in range error. If you do always, then you can check the timing on the mob and pally assistng. Target the mob at 5 yards, but no attacking. Push macro after 4 secs and see what happens. That should be enough time for the alt to get the mob targeted. If not, try: /cast [target=MainName-target] Judgement of Light. My guess is it takes longer to target a mob, than to cast a spell on it.

The next part is your alt is trying to target a wrong mob, but the option to continue to fight even if mobs change (in combat section of options, don't remember exact name), makes him attack the next thing that hits him. This is kinda low of happening unless the mob is hitting the alt.

Just take one step at a time. See if the alt actually assist correctly away from the mob. Then see if the spell works (already done). And then try closer to the mob. Somewhere you wil notice a patteren (doens't work in first .5 secs, but does later). Then you just have to adjust (like push button slower or put in a delay like: /castsequence [target=MainName-target] reset=combat/target , Judgement of Light

Hope that helps, good luck.