You still need to take the third party software out of the loop. The point of source on the first copy from CF card to macbook hard drive to imac HD needs to be straight forward with nothing else getting in the way.
Are the files corrupt when copying (drag and drop) on to the desktop from CF card to the iMac? If so then you've got hardware problems.
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Normally I'd agree with this... it's always a logical first step, and I always advise anyone to simply drag and drop files rather than using any app do bring them in. (How hard can it be, really, and it removes one source of exposure from the process).
But, in this case, the escalating nature of the problem, the additional corruption of files, in other apps, from other sources pretty much rules out any issues with the third party "ingesting" software.
I'd bet my bottom dollar on a hardware issue... hopefully a simple (cheap) one.