As title says I experience such problem after new feature with auto select files by % was implemented.
Example I've transfter with 3 files
Auto select select only only by 15% size rule, then I'm schoosing one more file manually.
(mod note: link removed)

When download is completed those files are stored in different directories and context menu option "open folder" shows only 1 file. Other is stored at source torrent file location.
(mod note: link removed)
And I don't have "Upon completion, move to this location" feature enabled.

I also wanna know what this setting does exactly, what happens If raised or lowered..

that is because with 'Auto' it moves the remaining file to the outer download folder and when you select another file to download, it doesnt move the file back. that is how it is supposed to work.