I'm not actually certain that Vinge gives any firm idea of how long the refugee ship took. However, let's assume for the moment you're right, and that it took a lot less time.
The best speculation I can make is that the priorities of the two ships were very different. The refugees were trying to get away as fast as they could from something that was extremely dangerous but not yet nearly at its full strength, before it could get too much stronger.
OOB2, on the other hand, already knew that the menace was at large and expanding rapidly. They had reasons to move very carefully. Their ship, as you point out, was damaged, which slowed them down. And lastly, they didn't know exactly where they were going. They had a general idea, but as I recall, they did not start out with an exact fix. All of these factors combine, I think, to suggest that they would be slowed down quite a bit.