When the dock is set to horizontal and the sub-docks perpendicular, the items/icons in each sub-dock are shown in a certain order (by user). But when the dock is changed to Vertical, the order of items in each sub-dock are now reversed.

Is there a setting to change the order depending on whether the dock is vertical or horizontal?

No. Order for horizontal docks is left to right, for vertical docks it's top to bottom.

I hope we’re talking about the same thing and if so, is that not backwards?

For example, on a horizontal dock, if I created a sub-dock on it and for the first item I add (and use the most), it will be closest to the main dock. Then I continue adding items to this sub-dock, which will be further away from the main dock (like the least used items). But when that main dock is changed to vertical, the order of the sub-dock is reversed and the least used items in the sub-dock are now closest to the main dock.

Simple: place the vertical dock on the left side of the screen instead of the right side. That way the sub-dock will open to the right and the first item will again be the one closest to the parent dock.

Look, I understand what you are saying (in fact the background of docks are normally adjusted for this), but you might be arguing for this, someone else will be arguing for the opposite (i.e. how it currently is).

As it is, horizontal docks ALWAYS go from left to right, and vertical docks ALWAYS go from top to bottom, regardless of the screen edge they are attached to and which screen quadrant they open into in the case of sub-docks.

People also don't usually keep switching their main dock from vertical to horizontal or vice-versa. Pick a position, adjust the items on sub-docks for that position (which you can do manually via drag & drop).

Fair enough, I didn't think of right side docking.

But it does do the oppostite of what you mention as I am docking on the left side and the dock will open to the right and the last item is the one closest to the parent dock. When it's docked on the right then it is first closest to main dock.

I'll just pick a spot and manually adjust...thanks