Clonezilla fails at cloning with mismatched GPT and MBR partition

Did you happen to use Apple's Disk Utility to create a FAT filesystem in that to-be-Windows partition? If so, you converted the disk from a legal GPT disk into a hybrid MBR disk, which OS X sees as GPT and Windows sees as MBR. The solution in this case is to clear the hybrid MBR data. A number of utilities can do this. I'll describe how to do it with my own GPT fdisk (gdisk) utility:

1. Download GPT fdisk from its Sourceforge page and install it. (Versions are available for Linux, OS X, and Windows. I'll assume you'll do this from OS X.) Alternatively, you could run it from a Linux emergency disc like Parted Magic.
2. Launch gdisk on your disk by typing sudo gdisk /dev/disk1 in a Terminal window. (Change the device identifier if it's not as you presented earlier or if you use another OS for the job.)
3. Type p to view the partition table to verify you're working on the correct disk. If not, type q to quit without saving your changes and try again with another device.
4. Type x to enter the experts' menu.
5. Type n to create a fresh protective MBR. Note that gdisk won't confirm a change; it'll just show you a new experts' prompt.
6. Type w to save your changes. You'll be asked to confirm this action. Do so.

With any luck this will fix the problem. If it doesn't, though, you can use gdisk's v option (on any menu) to have gdisk look for partition table problems. It can fix some minor problems automatically, but other times you'll need to make explicit changes. See the GPT fdisk documentation on GPT repairs for details.

El Capitan Addendum:

Apple's OS X 10.11 ("El Capitan") includes a new feature, known as "rootless" or "System Integrity Protection," which makes it difficult or impossible to run certain types of utilities, including GPT fdisk. To be sure, this new feature is intended to improve security by making it harder for malware to take control of the computer or for users to accidentally damage their own systems; but it also causes problems if you really need to use GPT fdisk or other third-party tools. If Apple's own tools permit removing a hybrid MBR, I don't know how it's done with them, so AFAIK this task really does require bypassing this new security feature.

There are several ways to work around this problem, such as:

• Use a non-OS X OS, such as an Ubuntu installer booted into its "try before installing" mode.
• Hold down Command+R as you boot your Mac to launch the Recovery environment, in which this feature is disabled. In theory, you should be able to run gdisk in this environment, although you might need to adjust the PATH environment variable. (I've not tried this approach, so there may be hurdles I've not considered.)
• Boot to the Recovery environment, open a Terminal window, type csrutil disable, and reboot into your regular environment. This action disables the rootless system. You can re-enable it by performing these steps but pass enable rather than disable to csrutil.

For more on the subject of the rootless environment, see this page.

Unless your new disk is over 2TiB, I strongly advise against attempting an MBR-to-GPT conversion on a Windows boot disk. The reason is that Windows ties its boot method (BIOS vs. EFI) to the disk type, so doing such a conversion requires switching from a BIOS-mode boot to an EFI-mode boot of Windows. If you're sure your firmware supports EFI, then this is at least possible, but it's still a hassle. See this page for details of how to do it. Basically, you need to use gdisk to do an MBR-to-GPT conversion, create a new EFI System Partition (ESP) to hold the EFI boot loader, and set up the EFI boot loader. You'll need to make similar changes in Linux, too, but they can be done a little more easily.