Why have some images a blue border and some other a yellow one?
The color of the border depends from the selection: blue border means that the image is "not selected", yellow border means that the image is "selected"; the viewer reads from ini file the default startup state. You can select images or clear the selection using left right button when it is configured to perform this kind of behaviour. There are two buttons on the application, one to select all the images and the other to deselect all the images. Some operations are possible only on selected images.

How can I Change the number of images in viewport?
Initial grid size is coded in ini file. You can click on grid button and change it.

What is the action associated with mouse buttons/wheel? How can I change it?
Mouse buttons and wheel action are customizable in the mouse tab simply by clicking on the desired behaviour.

Why the cineloop doesn't works?
There are two kind of cineloops: multiframe images cineloop and viewport images cineloop. Each multiframe image has his own control buttons (play, pause, stop). Cineloop of the opened images works only in 1x1 grid (you can view the viewport images in sequence using cineloop buttons).

Why some operations (windowing, flip, rotation, zoom, ...) have no effect to certain images?
Windowing and geometry actions (zoom, rotation, flip, ...) have effect only on selected images. Selected image have a yellow border.

Why some DICOM files are represented as a notepad icon?
When you see a notepad icon, the DICOM files contains a Structured Report (SR) instead of an image. You can read DICOM SR files in the table used to show DICOM Tags.