Short version: my iPad doesn't charge on my Mac Mini in Windows 7.
Long version: I have a Mid 2011 Mac Mini which I don't use a lot, and if I do it's usually in Windows 7 via Bootcamp. For interest sake I note that I upgraded the RAM from 2 GB to 8 GB for AUD$60 (instead of the several hundred dollars that Apple would have charged) and added an SSD M4 hard disk from Crucial (which was a qualified success) using an iFixit kit.
I also have an iPad 3, which shows that it's charging (and indeed does charge) in OS X, but when I boot into Windows 7 using Bootcamp the iPad does not charge, and it displays a message "Not charging." It indeed does not charge at least while the iPad screen is on, and appears to just maintain its charge when the screen is off.
Given that there are no hardware configuration changes during boot, I was a bit puzzled. The only explanation I could think of was that there is a mis-negotiation between the two devices about power. This Apple note confirmed that - http://support.apple.com/kb/HT4049. It's not a very helpful note because it says that "Some Apple computer (sic) and displays may offer the ability to operate more than one USB port at 1100 mA" but apparently it's a secret as to which computers and displays can do this.
Anyway, it turns out that I was correct - and Apple obviously doesn't think it's in their interests to do this properly when providing Bootcamp drivers. It's a pity that Apple can't write these very well. The note says "An Apple computer started up to Windows via BootCamp will not provide extra power."
It turns out that there is a fix for this, and it is provided by Asus. It's the Asus AICharger http://event.asus.com/mb/2010/ai_charger/ which allows you to "Quick charge your iPod, iPhone and even iPad". It's not limited to Asus products (obviously, since it works on my Mac Mini - as I write this it's just gone up 1% while the screen is on).
Another claimed feature is the ability to charge while in standby, suspend or shutdown modes. I haven't tested this, but if true it overcomes the standard limitations Apple has left in its software (http://support.apple.com/kb/HT4049).
Can it cause problems? I doubt it since it simply provides the same function as OS X does on the same hardware - i.e. it's a driver fix, but only time will tell...