Import into Subfolder
When importing, the check box "Into Subfolder" is checked and a folder named, but if you don't click the checkbox to uncheck it and then re-check it, it doesn't import into the subfolder even though it looks like it is going to. This happens to me multiple times a week as I am importing multiple projects everyday. Inevitablly several hundred photos randomly end up in the root folder during various imports throughout the week.

