I'm the author of Chess Position Trainer and found this thread just by chance as I was looking for some comments on Mihail Marin's new book “The Pirc Defence”.
Great to see my software discussed! First of all, I'm not a native speaker, but the confusion was created by a misleading statement regardless of the language. Instead of:
"You've just imported a PGN file. The imported moves are not in the correct order in the source."
it should say:
"You've just imported a PGN file. The imported candidate moves for your side might not be in the correct order in the source (e.g. a weaker move is shown first and the best move only as an alternative). In this case you can let CPT automatically re-order..."
I've just updated the text accordingly in the program for future releases.
I wan to note it is not a message dialog box. It is rather a flyout panel and you can click anywhere and it disappears. Actually, this function was added later as a "Tip" after an import has been completed. Giving some background: I personally purchased quite a few eBooks in PGN format in the past. After the import I realized that sometimes the author offers more than one candidate move for my side. However, not always was the author starting with the best move for my side, but with the move he is not recommending. In this case he usually uses the move evaluation "?" or "?!". If you start training your opening without making some adjustments you will train an inferior / bad move. Now, I thought it would be pretty helpful to automatically order the candidates based on these evaluations and thus saving a lot of time after the import. I do this after the import, because it can be that some candidate moves already exist for a position prior to the import. This gives more flexibility.
How can you find positions with more than one candidate move for your side? Of course there is a function, because I needed it myself too (sometimes I have to take advantage of the fact that I'm the developer of the software myself)
In the ribbon section "Navigation" there is a dropdown above two double blue arrows. The default selection is "Branch" and it let you navigate to the next / previous branch, which is the most common use case. However, you can also choose ">1 candidate move". If you select this entry and use the double blue arrows you will jump to the next position where more than one candidate move exists for your side. It is not only a big time saver for this use case, but also ensures you don't miss any such position, which is very difficult otherwise to detect.
I hope this clarifies a little bit the confusion.
Thanks,
Stefan