"MSI Slice Direction" should be enabled and should display "Ref C".

08:41 Apr 17, 2014 

My two cents.
In addition to the apparent 'passive' and 'active' distinction, any semantic differences that have come to mind are:

In "MSI Slice Direction" が有効化されて、"Ref C"を表示すること。,
有効化されて is used as a transitive verb, implying (clearly) that the function is enabled by some action or agent.

On the other hand,
in「MSI Slice Direction」が有効化し、「Ref C」を表示すること。,
有効化し is used as an adjective (to become enabled) or intransitive verb, technically not implying that the function is enabled by any action or agent, though some action or agent must be involved. But 有効化し is a usual, more natural way of expression in Japanese, in this kind of context, at least in the opinion of your reviewer.

I would agree with your reviewer, but cannot say for sure which version is "more" correct. At any rate, I can say your client is the boss.