I too was having issues with a Surface machine and IE with Qlik. I've found that I can not scroll in List Boxes or Chart Objects (but can make sections if it is viewable). Additionally, List Box values are conflicting that should not and do not on other devices/broswers that are based on set expressions for Time (Order vs Ship).
However, I've loaded Chrome, and all functionality works, but requires a little getting used to either using the mouse pad or swipe/touch.
I too have Sense Desktop running on a Surface Pro 3, and I am seeing different behaviour between this machine and my 2 year old Sony Vaio. In the script editor the tab key behaves very differently: on the Vaio it indents the script, but on the Surface Pro it moves focus to elsewhere in the window - this means that if I want to indent script I either need to type four space characters, or take my hands off the keyboard and click the indent script button. The other most noticeable difference is that I am getting no type-ahead help at all in either the script editor or the expression editor on the Surface Pro.
Does anyone know if there are any settings anywhere (either within Sense or in the Windows settings) that I could tweak to change this behaviour?
I also see different behaviour when I right click on objects in the user interface, but I am assuming that this is because the Surface Pro has a touch screen, while the Vaio doesn't.
I am running Windows 8.1 and Sense version 2.0.1 on both my Vaio and my Surface Pro.