That is no doubt odd, but I just wanted say that you should make sure your mouse pointer itself (not the folder icon you are dragging) is below the top edge of the dock before you drop the folder.
I have had cases of dragging it where the folder looks to be over the dock but then appears on the desktop when dropped- then when trying again I have noticed that about the mouse pointer itself.
Are there any items at all on the right side of your dock currently? If so, the best way to verify that you have dragged the folder far enough down is to notice that the existing items will move out of the way when your new item is in the correct drop zone-- if the existing items do not "move aside" and clear a spot for the new item you are not there yet.
Other than that, there is no preference anywhere that I have ever seen that would affect that fundamental operation of the dock so if the positioning of the icons is not it there well may be some deeper problems in your OSX installation.
BTW- are you able to add icons of applications themselves in the left side of the dock ok? If not, your dock itself may be locked- which can be done with a utility such as Onyx, Mac Pilot, etc. To add additional icons, the dock needs to be unlocked- but that is a long shot if you did not specifically lock it in the first place. Just grabbing at ideas here.