Background info for inexperienced users stumbling across this thread:
Doing the selection by moving the cursor left-to-right behaves slightly different from moving right-to-left. One direction is supposed to select all items that are touched by the selection rectangle; the other direction is supposed to select only items that are completely enclosed within the selection rectangle.
(Unfortunately, I can never remember which is which. I have been told that this is a common, unwritten, standard among CAD - and some other drawing programs. Mechanical guys under 30 were probably born knowing this. Us electrical guys over 60, fumble around until we seem to get the results we want. Superannuation strikes again.)
Left to right selects all item completely enclosed by the selection rectangle, while right to left is supposed to select all items touching this rectangle.
The latest seems to have issues (or at least isn’t intuitive on selected items - see above). I also noticed it also depends on using the high contrast mode or not (which is supposed to alter the user view only).
High contrast mode always limited selection to the active layer only. (Ok active layer is the wrong word. Active pcb side is more fitting as it also selects top footprints if you have top copper active in high contrast mode.)
In the above case, I used an test array of individual THT pads (so both copper sides are identical). But none of them have reference or value. I’m wondering if it is relevant regarding the selection ?
My guess would be those footprints have some invisible elements on other layer (maybe fab?) that get touched by your selection. Which should never be the case but it’s at least an explanation. High contrast mode may solve some of this if it ignores invisible layers.
After a closer examination, it seems to come from the Ref field located on the Fab layer ("%R"). Even if this fab layer is disabled (so its content is not visible to the user), it’s taken into account by the selection rectangle, which is totally counter-intuitive, and a bug to me.