While using the qimage comparator for checking the micro lens adjustments for a canon 5d II, I noticed the comparator would crop the images upon loading into the 2 window panes. 5616 x 3744 untouched jpeg images were being used, but I dont have no way of telling how much of a crop is being used. Is this a 100% crop that is opening?

I can take an image direct from the camera and use windows viewer for viewing, the image is no where near the size of the same images that are viewed in the comparator. I'm only guessing qimage is 100% larger then the windows viewer.
It doesn't matter, I can always use the magnifier to scroll down or up, and use the sliders for positioning the images, I was just curious what size the comparator images where when they are first opened. The comparator has come in handy for viewing the different lens adjustments side by side and that was what I was after anyway.

The size of the image you see, how much it overlaps the panels depends upon the monitor and screen resolution you have set.
If I have a monitor set to 1600 x 1200 and I insert an image into a comparator panel which is half as wide (since you have 2 panels,) I have 800 pixels to work with and I shoot for 5616, you can see how mucj image I see, and how much I have to scroll.
But, that's why you have the zoom out feature, to show your image at less than 100% size.

The Windows Picture viewer comes on with "Best fit" CTRL B, and offers Actual size, CTRL A.
That's only one image not two like the Qimage comparitor, and that is to large too for the allowed screen. So you have scroll bars there too.

Hope that clears some of it up for you.