Being a lapsed Catholic and someone who now, if forced to describe their practice, follows a path that combines Buddhist and Confucian principles, I can explain the problem. I once had a talk with a family friend who is a Priest and he explained the issue this way when I tried to argue that eastern and western practices were compatible. At the time I was still a practicing Catholic but had started meditation as a form of stress relief.
When one meditates, he said, in the Eastern method one is looking within for peace within ones self. However peace can only be found through God. One can not simply meditate in order to recognize ones true conditions, to "simply" allow negative emotion to wash away so that we can not only be better people ourselves but to then likewise treat others with more respect. No amount of meditation, he said, can melt away the Sin that separates us from each other, God and true peace.
The Bible, he said, even commands us to meditate but it commands us to mediate upon the Word of God and to reflect upon the Sins that seperate us from him.
Then, by extension, anything that is born of meditation is contrary to Biblical Teaching. We can not cultivate inner strength (Chi) alone, such strength is born from accepting God into your heart etc., etc, etc.
It gets even more touchy when you talk about finding enlightenment within. A standard retort is "if you could find enlightenment within Christ would not have been sent to us, the only path to enlightenment is through accepting Jesus Christ."
I agree with you, there should be a difference, bit Christian Theologians says otherwise.