Painting ports can be difficult. See, with the wood glue, if you don't sand, the color will look slightly different vs. where there isn't any wood glue. The paint will be glossier on the wood glue, so the key is try to keep that as clean as possible.
You also need to try to clear as much dust out of the enclosure as possible.
Alpine - C&D Tech - CT Sounds - Batcap - EA - eD- Rainbow