Hey there!
Sorry for your troubles. You know, I just did update to Yosemite this past week, after being on Mavericks for years. I kind of tried to stay behind the times since I figure most user issues would be with older stuff. Funnily enough, my 360 controller stopped working on Yosemite at all, and it wasn't until after your post I realized that had happened for some reason other than my recent installation of Parallels 10. My 360 controller is working fine on there.
Anyway, long story short, I updated my driver to a similar one to what you have, and now my controller works great in the other games I've tried from my Steam library. Like you, though, I'm having trouble with the bulk of the Arcen titles. Grr. However, The Last Federation and Stars Beyond Reach, both of which are on a newer version of unity 3D, both work fine with it. So it's something to do with the older version of unity the other games are compiled with.
Ironically, apparently the v5 unity builds that some other games are using, which are newer than what we choose to use even for our latest games, are again broken on Yosemite for the 360 controllers. Woohoo... so I expect we'll run into other unity 3D games that are busted for these controllers in our respective libraries.
Anyway, all of this is a roundabout way of saying that I can duplicate your problem, and that:
1. The earlier version of unity 4.x does have this problem (but only on Yosemite), and that's what this game is on.
2. The later versions of unity 4.x do not currently have that problem, and that's what I'll upgrade this to this week.
3. The even-later versions of unity, the 5.x branch, apparently have this problem anew (again only on Yosemite). I don't plan on upgrading to them.
There is an external input manager called Rewired that I really want to start using, and backport into our older titles as well. It's a lot more flexible in a lot of different ways, works on all of the above versions of unity, and doesn't have any compatibility issues of these sorts. So, longer-term that's going to be my solution, but in the short term a simple unity version upgrade on my part ought to do the trick.
I'll post here again when I have an actual fix for the current problem, hopefully tomorrow. But I figured I'd go ahead and let you know what I've found so far. Thanks for your patience!