For a long time, I have been having this glitch. Instead of dropping one item at a time, I drop a stack of items. It might just be something really easily solved that I just wasn't smart enough to find, but I haven't found anything. It gets really annoying having to sort your inventory to throw single items.
Turn off sticky keys off. If you hold control while dropping items, it will drop the whole stack. Sticky Keys is a Windows feature that simulates the holding of certain keys when you double-tap them. Turning this "feature" off will fix your problem.
Item Dropping Glitch?