I found a work around by moving the T120 after the second V0, not before it.
Player player = new Player();
player.play("T60 V0 A3q B3q C3q B3q V1 A2h C2h | V0 T120 A3q B3q C3q B3q V1 A2h C2h");
In general, I used the following regex to post-fix my tempos when reading in from a MusicXML file:
Pattern tempoFixedPattern = new Pattern(pattern
.getMusicString().replaceAll("(T[0-9]+) (V[0-9]+)", "$2 $1"));