There are many cases of Wubi virtual disk corruption. The exact cause is unclear to me although I suspect in many cases it's the forced shutdown/reboot of the Wubi Ubuntu install. There are some cases where the affected users insist that they did not force shutdown so, the truth is - I don't know exactly. But what I do know is that my blog page to correct this problem is the most visited page by far, so it does affect many people.
That's why I recommend that if you need to store data you should do it on the /host partition (NTFS) as separate files, rather than all stored together in the virtual disk (that is really just one file). It's simply a question of risk, whether that file is deleted by accident or corruption, you have all your eggs in one basket.
What I also recommend is synchronize the data you do keep on the Wubi install to Ubuntu One. So in that way you can have the convenience of Wubi without the risk.
The 32GB limit on the script (which I maintain) is based on the 30GB limit built into Wubi. I have no specific reason or knowledge that anything over this will be more susceptible to corruption (and personally I doubt that it makes any difference), but I don't believe people should be encouraged to create 100GB virtual disks because of the risk. That's the reason.
I've written about this on my blog which I encourage you to read if you have more questions: