Quite weird behavior there.

I know quite a few people switched to IS Boxer for the pvp effectiveness.
The FTL functionality, in particular combined with instant window swap.

And used a /Castsequence [Target=Focus] Flame Shock, Lava Burst, Chain Lightning, Frost Shock

Specifically so they could be burning one target down, notice their Focus target come into the middle and then burn the focus down, without switching targets.

With the [@Focus], you are telling Warcraft what to target, without telling the toon to change their target.
So IS Boxer has the toon continue to target whatever the main toon is targeting, via the FTL Assist.
I've had toons who heal via assisting the mob /cast [Target=TargetTarget] SomeHeal, and have no issue with the spell going to someone (according to the [Target=Whatever] despite FTL having my toon target something else).

Do you have any other addons that could be causing the conflict?
It's quite odd that /Cast [Target=Focus] fails...