Limitations
Compared with a regular installation, a Wubi installation faces some limitations. Hibernation is not supported and the filesystem is more vulnerable to hard reboots. Also, if the Windows drive is unmounted uncleanly (Windows crash, power failure, etc.), Ubuntu will not be able to repair, re-mount, and boot from the Windows NTFS drive until Microsoft Windows has successfully booted, repaired the drive, and then shut down cleanly. If the Windows system could not be booted after the corruption to repair the filesystem, the user would also not be able to boot Ubuntu.
Performance related to hard-disk access is also slightly slower, more so if the underlying disk image file is fragmented, on a Wubi install compared to a normal one.
Wubi creates the root.disk file using Microsoft's proprietary NTFS file system while running under the MS Windows OS and then while the Ubuntu OS is running it accesses that file using an alternate file system driver. The differences between the Microsoft and Linux implementations of NTFS could technically result in corruption of the root.disk file that affects the NTFS filesystem in such a way that it could even prevent Windows from booting. Running chkdsk /r from MS Windows to fix the damaged NTFS file system and then shutting down Windows cleanly may fix any corruptions (this may take a significant amount of time to run as root.disk is a large file).
Read more about this topic: Wubi (Ubuntu Installer)
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