I am wanting to extend my windows partition to occupy some unallocated space. When I use gparted in ubuntu it says there is something wrong with the file system and refuses to work the operation. But when I boot into the windows os that is on the partition I am wanting to change it will do it fine. Would it be a bad idea to use windows to partition the partition it is currently running on?
Not at all, I have extended and shrunk from Windows just fine!
I am a bit concerned that Gparted is having issues though... Possibly make sure you are using the latest version and/or do a can of the hard drive to make sure there are not any other errors.