Hi Andrés,
I have fixed most of these problems---the ones that can be fixed---and a few more in an update I've just released for all platforms.
Red: The title of group boxes is not aligned well vertically. This happens in Win7 but not in Linux.
This has been fixed with the update. Just a matter of fine tuning margins (each platform has its own typographic idiosyncrasies).
Green: The horizontal scrollbar in list boxes overlaps the border. This happens both in Win7 and Linux.
Unfortunately, I cannot fix this one. It is a Qt bug (incorrect z-order of styled scroll bars). This bug does not happen on Mac OS X / Cocoa.
Blue: Sometimes the height of the list of comboboxes is not sized well. This happens both in Win7 and Linux.
Same as above: it is a Qt bug, and happens on all platforms.
Besides the group box problem, I have fixed a few more, notably a bug that was setting a wrong height for the command line control.
Thank you for detecting these issues.