I can't think of any exceptions to this off the top of my head, so my inclination is to tell you that this is always the case (though that's risky, with English having as many exceptions as it does...)
As for the other one --
the correct structure is this:
Not only are taxes collected on A, but also on B.
In A, we have
not only are taxes on A collected but also on B - which doesn't make sense.
In C, we have a similar issue.
In D, we have
not only taxes on A are collected but also on... again- pretty nonsensical, and a bad placement of "are collected"
And in E, we're missing an "on" to make this one make sense.