Booting from external linux drive destroyed internal windows installation?

Question

I have installed Arch Linux on an external SSD. I have already used it for some time without errors to use my own arch Linux installation on other machines.

Now I started using two different computers which have windows installed on their internal drives and here, booting from my drive seems to effect the windows installation. When I boot windows after having booted Linux, sometimes the “Windows startup repair” loads but finds no errors and windows starts normally. Now on one of the machines however, Windows starts loading but after a few seconds crashes with a blue screen. I was able to repair that by loading a restore point but after booting Linux a few times the blue screen came back.

I did not mess with the windows drive from within arch Linux. Windows was running fine for a couple of years on both machines.

What could have happened? It seems to me, that Linux has changed something on the internal drive by itself. As far as I understand booting, this is the only way something like this could happen. Or am I wrong?

I am a bit worried because I would like to use my drive without the fear of destroying other installations of operating systems.

More info:

• The machine is a Dell studio 1558, running windows 7. I don't remember the type of the one where everything worked fine, but it was a newer model. Might have been a Dell as well though.
• I am using BIOS, not UEFI.
• Yes, I boot into Arch by choosing the external usb drive through BIOS.
• I am running devmon to automount drives. However I did not install ntfs-3g which is necessary to write to ntfs-drives as far as I know. It automounts my external drive from which I am booting once more in /mnt but not the internal drive. I am also running laptop-mode-tools. I can't think of any more services that have something to do with the internal drive. Oh yeah, and I ran grub-mkconfig -o /boot/grub/grub.cfg a few times.