I ran into that last year using purchased hay as mulch. I noticed the effects within a few weeks and pulled up all the hay, but I did lose some annuals and a few plants in my vegetable garden (fortunately, I hadn't used much in with the vegs). The permanent plants all had deformed growth last year, but this year they all look nice and healthy. I think mine recovered so quickly because I only had it on the soil surface and for such a short time. It's my understanding that once it is mixed in with the soil it can take years to recover.

Of course, both the company I bought the hay from and the hay grower denied having used any sort of herbicide on the hay, but my plants showed otherwise. The experience has left me really gun-shy about using any organic matter that doesn't come from my own place.