I have a dual boot Ubuntu 14.04<>Windows 10 system. It has two SSD-drives, 256 GB for Windows and 128 GB for Ubuntu and one 1 TB HDD for data. Ubuntu works without any problems, Windows 10, however, often hangs for minute long periods something that is very annoying. If I physically remove the Ubuntu SSD Windows seems to be ok, also if I via BIOS, skipping GRUB, boot directly into Windows the problem seems to disappear. I would like to understand what causes the problem and what I can do about it. Thanks in advance for any tip. H
PS The upside is that I now prefer working with Linux.
Can't write comments to your main question due to low reputation points. I wanted to tell you that (or at least it used to be) windows will boot fine when it sees its partition as "active".
Let's say you're going to install Windows: First you boot onto your disk and this will report an error about "missing operating system". Perfect! at this point the disk/partition is marked as Active. Now you can reboot and continue installing Windows. Windows bootloader will be installed on that disk.
Linux does not care. You can install its bootloader on a old floppy if you wish..
But this is probably a cause why your Windows have difficulties booting when another disk is inserted.