THE SHORT of IT
Entering moves by either clicking the source square first or by clicking the destination square first are not consistently equivalent.
THE LONG of IT
First a few preliminaries (a scenario and some definitions) so I can state the problem more simply. Sorry for the verbosity (which I was told was a good thing).
TWO TYPES of NAVIGATING the MOVELIST
I am studying a game in my database. I usually navigate its movelist by scrolling the mouse wheel. (Everything is fine so far.)
[: Lets call this 'Explicit Navigation', since I'm using Scid's unambiguous navigation controls.]
After I have gone through a particulalry interesting game, I sometimes rewind it and then test my memory of it [: Training] by making the moves on the board myself, knowing that a dialog [: the Add Variation Dialog, for want of a better name] will pop up if my move is wrong (i.e. differs from the move in the movelist).
[: Lets call this 'Implicit Navigation', since Scid has to interpret my input (contextually) to understand that I don't want to (lets say) truncate the game here but simply advance to the next move in the movelist (if there is one) or append the move to it (if there isn't).]
THREE TYPES of MAKING MOVES on THE BOARD
Now, I can make a move on the board in two distinct ways: by clicking squares [: Clicking Method] and by dragging pieces [: Dragging Method]. Normally I drag. (Again, everything is fine.)
The Clicking Method can be subdivided further into two ways of clicking the squares: A to B or B to A. If for example I wanted to move 1.e4, I could do this either by (i) clicking e2 and then e4 [: Forward Clicking Order], or by (ii) clicking e4 first and then e2 [: Backward Clicking Order].
(In some rare cases I will use Forward Clicking Order and everything would continue to be fine.)
THE PROBLEM (or FEATURE?)
I am Training a game. Lets say Topalov-Gelfand, Linares 2010. The opening is the Petroff. I want to minimize my mouse movements so I am using Implicit Navigation. White is at the bottom so I do 1.e4 in Forward Clicking Order and 1...e5 in Backward Clicking Order. But at my last input the Add Variation Dialog pops up.
Even worse: If one chooses "Add New Variation" the game will add the move as if it were a bonafide variation, even though it is the mainline move. However, this could also be seen as a feature, since it adds a visually distinct way of adding variations to the movelist.