The first stage of the Windows bootloader cannot read compressed NTFS files. These files include BOOTMGR and NTLDR, which are used for the second stage of the Windows boot process. If they are in fact compressed, an error message like the following would be returned:
[NTLDR|BOOTMGR] is compressed
Press Ctrl+Alt+Del to restart
Try booting from a Windows installation or recovery disk, then use the command prompt to decompress the files—running
/U /I NTLDR BOOTMGR DZNRX on the root directory of the system partition might fix the problem. If required, repeat the process for any other files the system complains about.