Jeff, the glazing compound will "never" dry. It is made to stay flexible "forever" in window frames. In reality, it gets hard in a year or 2, but it is a slow process. Minwax Wood Filler is a much better product if you are painting and Bondo will also work. The Bondo is cheaper if you have a lot of filling to do. Neither Bondo or Minwax Wood Filler take stain well and Minwax has a colored "putty" type product in a jar and also "Magic Marker" like stain that does an excellent job of disguising the wood filler if you play with it a while. If you used the window glazing for interior furniture, paneling or molding, I would change it.
Now the good news, if you just filled some small exterior nail holes with window glazing, it should be solid enough that you can paint over it by now.