You install NTFS for Mac, restart the system, and the Startup Disk utility in System Preferences no longer shows your Windows partitions.
The stock Startup Disk utility only shows NTFS partitions mounted by the stock read-only NTFS driver. When you install our NTFS for Mac, NTFS partitions are mounted with our driver, and won’t show up in the native selector. It’s an internal limitation of OS X.
To circumvent that, we include our own startup disk selector that only shows NTFS partitions mounted with our driver.
In other words, to set a Windows partition as bootable, you’ll need to use the boot selector in the NTFS for Mac preference pane instead of the stock selector.
First, select BOOTCAMP partition in the list. Make sure the disk is mounted. Now press Set as startup… button. Your Mac will boot from the selected disk after restart.
Alternatively, you can hold Option when starting up. This puts you into a boot menu displaying your OS X and Windows partitions.
It should be noted that the NTFS for Mac boot selector doesn’t work for Boot Camp configurations using a pure GPT disk layout instead of hybrid GPT. This applies to Macbook Airs from mid-2013 and later, and Macbook Pros and Mac Pros released in late 2013 and beyond. On those systems, you need to use the Option boot selector for booting into Windows, unless it’s installed to a pure MBR disk.