First of all I want to say I really like the software, and I hope I can reinstall it in the future.
To do so I would request an option (maybe a commandline switch) to completely disable all USB features (autodetect, printing, everything else...), so all communication with the printer would be via SD-card.
Currently I can't use Cura, because whenever I start it it seems to run its autodetect feature to look for printers. The problem with this is that I have a (very old) fan controller which is connected to my PC via USB, using an FTDI USB to serial chip (i.e. something very similar to the communication in a 3D printer). And apparently Cura sends some commands while autodetecting which are interpreted by my fan controller. These commands cause a change in one of the alarm temperature thresholds, which causes the alarm to go off.
So when I first installed Cura i spent an hour frantically searching for the error (and then searching for the software for the fan controller), while my PC was emitting a loud beep every 3 seconds.
The fan controller is a "T-Balancer BigNG", the company making it stopped supporting it years ago. However it is still working perfectly for me, controlling the fans in my PC.
As a workaround I could disconnect the fan controller and run it in standalone mode.
On the other hand it does seem a bit problematic that Cura's autodetect is causing random commands to unrelated devices. The arduino IDE and printrun/pronterface did not cause any problems. I did hit "connect" both in arduino and Pronterface while COM3 was selected (the port for my fan controller, the printer was on COM4), and neither caused any problems. Though I am sure I would have had all kinds of trouble if I had sent Marlin to the fan contoller.
To be sure I even ran Cura again after I had set the alarm value back to the proper setting, and the problem came back. So it definitely is Cura messing with the settings of the fan controller.
edit: changed title to the actual question