I'd vote for Linux as well. About 6 months ago I installed Linux Mint (my first real intro to the OS). Completely facinated by it. It did everything. Easy to install, GUI based for a Windows guy like me. Fast, needed next to no hardware. Windows is bloated. And Windows Server 2012 just tries to be a Linux by not installing the GUI unless asked. But it's incredibly difficult and still not user friendly.
Linux is my suggestion too. It one can avoid Windows, system may be more stable. Also why not use ony ethernet connection and some script to control and acquire data from T and M device? This is easy and more transparent.
Honestly, I have found that almost all current generation OS's have the same amount, just different issues. I have found that with windows, as long as you are using the software withing the min hardware recomendations that I cannot remember the last time that I had a blue screen. The last time I got an actual blue screen was because I had a failing CPU (ane yes it was a cpu failure, all parts ended up getting swapped out in the system, and when the cpu was swapped, it all worked as appropriate). I have had a few lockups, but this was not the fault of windows, but a porly designed program that had memory overflow issues. An OS can try and mitigate the failure of others, but it is not their responsibility to stop them from doing stupid stuff. The other computers that I have dealt with that have issues lockig up is because they failed to install an anti-virus. In this day and age, any OS that has enough market penetration will deal with viruses. Many of the targets are chosen based upon economics rather than ease of hacking.
Until now i did *never* use Windoze in one of my test setups. It is silly to do so: Lots of serious software companies are out there capable of helping you out with proper tools that do not crash all the time...