I've actually been having similar problems with WUBI. For some reason this past week, I decided to increase the size of my ubuntu partition by reinstalling it. Of course, this deleted all of my data on that partition that I stupidly forgot to back up. Nothing crucial, so whatever. But for some reason, the new partition has problems installing and will either crash, boot up to GRUB, or if the reinstallation finally works, it runs incredibly slowly. I'll open Firefox or open a directory and the screen will go gray and unusable for a minute. Updating it helped it with the slowness issues slightly; now it only freezes when I open firefox and a directory simultaneously. Of course, for some inexplicable reason, that barely usable partition also stopped working the next time I booted it.
Not to mention when I first time I tried to reinstall(some time this weekend, I think it was Saturday or Sunday), WUBI installed ubuntu 13.04(???) for some reason. This OS didn't have any problems with speed at all as far as I could tell. The only problem I had with it was that I could only log in as guest. The newest version of WUBI forces you to include a username and password when you're installing, so you already have an account set up when you load up Ubuntu for the first time. However, 13.04 didn't have the default profile set up so I had to choose which user to log into. The account that I set up in WUBI didn't work.
What the fuck Ubuntu why is everything breaking. This is literally the only time I can think of in the past 2-3 years of using Ubuntu that I've had a serious problem. It's like all those times I probably should have been suffering computer bullshit but didn't has finally caught up with me.
So yeah, dunno if you're also using WUBI (and I dunno if that's the problem, I might've gotten these same issues if I installed a fresh copy of ubuntu over my entire hard drive), but it seems like they've been having some problems or something.