A quick yahoo search, "flies in straw" turns up a lot. See for example,
this from Illinois Department of public health and there are others.
The first thing I'd ask is what kind of flies they are. The site above should help. Next, what's the source?
I have never had a problem with flies in straw or in rotted manure, (or my compost pile for that matter) but it sounds like it's possible. The bottom line is that females will lay eggs in rotting straw or manure. I take it that you bought bags of rotted, composted manure, from some store, right? I would think that the rotted composted manure was produced in such a way so as to heat it to a temp that would have killed the eggs. (Do you have an unopened bag you could slit open and see if flies emerge?) The straw could be a problem, I suppose.
Finally would be how to get rid of them, if they don't disperse on their own. For this I'll defer to the real experts here. Has anyone else ever had this problem? If you track Lukky7's posts, you'll see it's a new garden and all of our advise is being taken to heart. I don't know what to say about the fly problem.