It's hard to say without looking at an actual example, but I think you might be experiencing this problem. The font metrics allow the font to run outside its container, and a bug in Chrome prevents these parts from recieving the hover color.
Try setting a background color on the element to see if there are any pixels actually running out of the element. To fix it, you'd need to make the element really wrap the text (by giving it a top padding, for example.)