I've been having this problem with my randomly generated play queues, but it applies to manual play queues as well.
To reproduce:
1) Queue Up Track 1
2) Queue Up Track 2
3) Queue Up Track 1
4) Queue Up Track 3
5) Play track 1
6) Advance player to next track (either by listening or skipping)
7) [Track 2 starts playing]
8 ) Advance player to next track
9) [Track 1 starts playing, with both the first and third items in the queue with the play icon next to them]
10) Advance player to next track
11) [Track 2 starts playing]
12) Goto 8